Mercurial > repos > iuc > snpfreqplot
changeset 0:1062d6ad6503 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/heatmap_for_variants.R Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,212 @@ +#!/usr/bin/env R + +suppressPackageStartupMessages(library(pheatmap)) +suppressPackageStartupMessages(library(RColorBrewer)) +suppressPackageStartupMessages(library(tidyverse)) + +fapply <- function(vect_ids, func) { + #' List apply but preserve the names + res <- lapply(vect_ids, func) + names(res) <- vect_ids + return(res) +} + + # M A I N +stopifnot(exists("samples")) +variant_files <- fapply(samples$ids, read_and_process) # nolint + +extractall_data <- function(id) { + variants <- variant_files[[id]] + tmp <- variants %>% + mutate(posalt = uni_select) %>% + select(posalt, AF) + colnames(tmp) <- c("Mutation", id) + return(tmp) +} + +extractall_annots <- function(id) { + variants <- variant_files[[id]] + tmp <- variants %>% + mutate(posalt = uni_select, + effect = EFF....EFFECT, gene = EFF....GENE) %>% + select(posalt, effect, gene) + return(tmp) +} + + # process allele frequencies +processed_files <- fapply(samples$ids, extractall_data) +final <- as_tibble( + processed_files %>% + reduce(full_join, by = "Mutation", copy = T)) + +final <- final[str_order(final$Mutation, numeric = T), ] %>% + column_to_rownames("Mutation") ## sort and set rownames +final[final < variant_frequency] <- NA ## adjust the variant frequency: +final <- final[rowSums(is.na(final)) != ncol(final), ] +final <- t(final) +final[is.na(final)] <- 0 +class(final) <- "numeric" + + # add annotations +## readout annotations +processed_annots <- fapply(samples$ids, extractall_annots) +ann_final <- processed_annots %>% + reduce(function(x, y) { + unique(rbind(x, y))}) %>% + filter(posalt %in% colnames(final)) ## apply frequency filter +ann_final <- as_tibble(ann_final[str_order( + ann_final$posalt, numeric = T), ]) %>% + column_to_rownames("posalt") ## sort + + # rename annotations +trans <- function(x, mapping, replace_missing=NULL) { + # helper function for translating effects + mapped <- mapping[[x]] + if (is.null(mapped)) { + if (is.null(replace_missing)) x else replace_missing + } else { + mapped + } +} + +# handle translation of classic SnpEff effects to sequence ontology terms +# The following list defines the complete mapping between classic and So effect +# terms even if not all of these are likely to appear in viral variant data. +classic_snpeff_effects_to_so <- list( + "coding_sequence_variant", "coding_sequence_variant", "disruptive_inframe_deletion", "disruptive_inframe_insertion", "inframe_deletion", "inframe_insertion", "downstream_gene_variant", "exon_variant", "exon_loss_variant", "frameshift_variant", "gene_variant", "intergenic_variant", "intergenic_region", "conserved_intergenic_variant", "intragenic_variant", "intron_variant", "conserved_intron_variant", "missense_variant", "rare_amino_acid_variant", "splice_acceptor_variant", "splice_donor_variant", "splice_region_variant", "5_prime_UTR_premature_start_codon_variant", "start_lost", "stop_gained", "stop_lost", "synonymous_variant", "start_retained_variant", "stop_retained_variant", "transcript_variant", "upstream_gene_variant", "3_prime_UTR_truncation_+_exon_loss_variant", "3_prime_UTR_variant", "5_prime_UTR_truncation_+_exon_loss_variant", "5_prime_UTR_variant", "initiator_codon_variant", "None", "chromosomal_deletion" +) +names(classic_snpeff_effects_to_so) <- c( + "CDS", "CODON_CHANGE", "CODON_CHANGE_PLUS_CODON_DELETION", "CODON_CHANGE_PLUS_CODON_INSERTION", "CODON_DELETION", "CODON_INSERTION", "DOWNSTREAM", "EXON", "EXON_DELETED", "FRAME_SHIFT", "GENE", "INTERGENIC", "INTERGENIC_REGION", "INTERGENIC_CONSERVED", "INTRAGENIC", "INTRON", "INTRON_CONSERVED", "NON_SYNONYMOUS_CODING", "RARE_AMINO_ACID", "SPLICE_SITE_ACCEPTOR", "SPLICE_SITE_DONOR", "SPLICE_SITE_REGION", "START_GAINED", "START_LOST", "STOP_GAINED", "STOP_LOST", "SYNONYMOUS_CODING", "SYNONYMOUS_START", "SYNONYMOUS_STOP", "TRANSCRIPT", "UPSTREAM", "UTR_3_DELETED", "UTR_3_PRIME", "UTR_5_DELETED", "UTR_5_PRIME", "NON_SYNONYMOUS_START", "NONE", "CHROMOSOME_LARGE_DELETION" +) +# translate classic effects into SO terms leaving unknown terms (possibly SO already) as is +so_effects <- sapply(ann_final$effect, function(x) trans(x, classic_snpeff_effects_to_so)) + +# handle further translation of effects we care about +so_effects_translation <- list( + "non-syn", "syn", + "deletion", "deletion", "deletion", + "insertion", "insertion", "frame shift", + "stop gained", "stop lost" +) +names(so_effects_translation) <- c( + "missense_variant", "synonymous_variant", + "disruptive_inframe_deletion", "inframe_deletion", "chromosomal_deletion", + "disruptive_inframe_insertion", "inframe_insertion", "frameshift_variant", + "stop_gained", "stop_lost" +) +# translate to our simple terms turning undefined terms into '?' +simple_effects <- sapply(so_effects, function(x) trans(x, so_effects_translation, replace_missing = "?")) +# complex variant effects (those that do more than one thing) are concatenated +# with either '+' (for classic terms) or '&' (for SO terms) +simple_effects[grepl("+", so_effects, fixed = TRUE)] <- "complex" +simple_effects[grepl("&", so_effects, fixed = TRUE)] <- "complex" +simple_effects[so_effects == ""] <- "non-coding" + +ann_final$effect <- simple_effects +ann_final$gene <- sub("^$", "NCR", ann_final$gene) + +## automatically determine gaps for the heatmap +gap_vector <- which(!(ann_final$gene[1:length(ann_final$gene) - 1] == # nolint + ann_final$gene[2:length(ann_final$gene)])) + + # colormanagement +my_colors <- colorRampPalette(c("grey93", "brown", "black")) #heatmap +count <- length(unique(ann_final$gene)) #annotations (genes) +gene_color <- c(brewer.pal(brewer_color_gene_annotation, n = count)) +names(gene_color) <- unique(ann_final$gene) + + # colormanagement annotations (effect) +## Define the full set of colors for each effect that we can encounter +## This is not bulletproof. The effect names given here were swapped into the +## data (see above substitutions in ann_final$effect) and so are hard-coded, +## as well as their preferred colors. + +all_colors <- data.frame( + color = c("white", "green", "orange", "red", + "black", "grey", "yellow", "blue", "purple", "brown"), + name = c("non-coding", "syn", "non-syn", "deletion", + "frame shift", "stop gained", "stop lost", "insertion", + "complex", "?")) +## Reduce the full set to just those that we want +detected_effects <- unique(ann_final$effect) +subset_colors <- subset(all_colors, name %in% detected_effects) +effect_color <- subset_colors$color +names(effect_color) <- subset_colors$name +color_list <- list(gene_color = gene_color, effect_color = effect_color) +names(color_list) <- c("gene", "effect") + + # visualize heatmap +if (pheat_number_of_clusters > length(samples$ids)) { + print(paste0("[INFO] Number of clusters: User-specified clusters (", + pheat_number_of_clusters, + ") is greater than the number of samples (", + length(samples$ids), ")")) + pheat_number_of_clusters <- length(samples$ids) + print(paste0("[INFO] Number of clusters: now set to ", + pheat_number_of_clusters)) +} + +get_plot_dims <- function(heat_map) { + ## get the dimensions of a pheatmap object + ## useful for plot formats that can't be written to a file directly, but + ## for which we need to set up a plotting device + ## source: https://stackoverflow.com/a/61876386 + plot_height <- sum(sapply(heat_map$gtable$heights, + grid::convertHeight, "in")) + plot_width <- sum(sapply(heat_map$gtable$widths, + grid::convertWidth, "in")) + return(list(height = plot_height, width = plot_width)) +} + +height <- round(max(c(max(c( + 16 * (length(unique(ann_final$effect)) + + length(unique(ann_final$gene))), 160)) / + nrow(final), 15))) +width <- round(ratio * height) + + +if (!(out_ext %in% c("svg", "jpeg", "png", "pdf"))) { + stop("Unknown extension: ", ext, ", aborting.") +} +plot_device <- get(out_ext) + + +## A constant scaling factor based on the calculated dimensions +## above does not work for PNG, so we resort to feeding pheatmap +## with a direct filename +plot_filename <- NA +if (out_ext %in% c("jpeg", "png")) { + plot_filename <- out_file +} + +## SVG is not a format pheatmap knows how to write to a file directly. +## As a workaround we +## 1. create the plot object +## 2. get its dimensions +## 3. set up a svg plotting device with these dimensions +## 4. print the heatmap object to the device +hm <- pheatmap( + final, + color = my_colors(100), + cellwidth = width, + cellheight = height, + fontsize_col = round(1 / 3 * width), + fontsize_row = round(1 / 3 * min(c(height, width))), + clustering_method = pheat_clustering_method, + cluster_rows = pheat_clustering, + cluster_cols = F, + cutree_rows = pheat_number_of_clusters, + annotation_col = ann_final, + annotation_colors = color_list, + filename = plot_filename, + gaps_col = gap_vector +) + +if (out_ext %in% c("pdf", "svg")) { + plot_dims <- get_plot_dims(hm) + plot_device(out_file, + width = plot_dims$width, + height = plot_dims$height) + print(hm) + dev.off() +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/helperFunctions.R Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,94 @@ +#!/usr/bin/env R + +## Helper functions for processing variant data, especially for +## data which contains duplicate variants differing only on +## annotation. + +difference_in_group <- function(lines) { + #' Find the columns containing the differences between a + #' group of lines sharing the same POS and ALT. + #' e.g. + #' CHROM POS REF ALT IMPACT FUNCLASS AA GENE + #' 1 NC_045512.2 3037 C T LOW SILENT F924 ORF1ab + #' 2 NC_045512.2 3037 C T LOW SILENT F106 ORF1ab + #' 3 NC_045512.2 3037 C T MEDIUM SILENT F106 ORF1ab + #' + #' should yield: + #' + #' unique.name + #' 1 3037 T (LOW|F924) + #' 2 3037 T (LOW|F106) + #' 3 3037 T (MEDIUM|F106) + #' + #' i.e. it identifies that IMPACT and AA are the differing + #' columns for each of the rows + #' + #' Ideally this function should just be used as + #' ``tab %>% group_by(POS, ALT) %>% difference_in_group()`` + #' + diff.colnames <- c() + nlines <- nrow(lines) + if (nlines > 1) { + for (i in 1:(nlines - 1)) { + test1 <- lines[i, ] + for (j in i:nlines) { + test2 <- lines[j, ] + diff.colnames <- c(diff.colnames, + names(test1[!(test1 %in% test2)])) + } + } + } + uni_select <- c("POS", "ALT", diff.colnames) + return(lines[, uni_select] %>% unite(uni_select, sep = " ")) # nolint +} + +split_table_and_process <- function(tab) { + #' Split TAB into groups sharing the same POS and ALT + #' and create distinguishing labels. + #' + #' Calls the above ``difference_in_group`` for each + #' discovered group. + #' + #' This function is necessary because tidyr is difficult + #' to write custom group binding functions. + posalts <- tab %>% group_by(POS, ALT) %>% select(POS, ALT) # nolint + nlines <- nrow(tab) + groups <- list() + groups[[1]] <- c(1, 1) + last_pa <- paste(posalts[1, ]) + for (r in 2:nlines) { + curr_pa <- paste(posalts[r, ]) + posalt_diff_between_lines <- !all(last_pa == curr_pa) + if (posalt_diff_between_lines) { + ## end of current group, start of new + groups[[length(groups)]][2] <- r - 1 ## change prev end + groups[[length(groups) + 1]] <- c(r, r) ## set (start, end) + } else if (r == nlines) { + ## i.e. if the very last line shares + ## the same POS ALT as the one before, + ## close current group. + groups[[length(groups)]][2] <- r + } + last_pa <- curr_pa + } + as_tibble(do.call( + "rbind", + lapply(groups, function(grange) { + expand_range <- grange[1]:grange[2] + difference_in_group(tab[expand_range, ]) + }) + )) +} + +read_and_process <- function(id) { + file <- (samples %>% filter(ids == id))$files # nolint + variants <- read.table(file, header = T, sep = "\t") + uniq_ids <- split_table_and_process(variants) + if (nrow(variants) != nrow(uniq_ids)) { + stop(paste0(id, " '", file, "' failed: ", file, "\"", + "nrow(variants)=", nrow(variants), + " but nrow(uniq_ids)=", nrow(uniq_ids))) + } + variants <- as_tibble(cbind(variants, uniq_ids)) # nolint + return(variants) +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEffExtract.R Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,94 @@ +#!/usr/bin/env R + +suppressPackageStartupMessages(library(VariantAnnotation)) +suppressPackageStartupMessages(library(tidyverse)) + +tsv_eff_from_vcf <- function(input_vcf, output_tab) { + read_vcf <- readVcf(input_vcf) # nolint + chrom_pos <- data.frame(read_vcf@rowRanges)[, c("seqnames", "start")] + ref_alt_filter <- read_vcf@fixed[, c("REF", "ALT", "FILTER")] + dp_af <- read_vcf@info[c("DP", "AF")] + + ## Unwrap the DNAStringList + # nolint start + ref_alt_filter <- data.frame( + REF = as.character(ref_alt_filter$REF), + ALT = sapply(seq_len(nrow(ref_alt_filter)), function(i) { + as.character(ref_alt_filter$ALT[[i]]) + }), + FILTER = as.character(ref_alt_filter$FILTER)) + # nolint end + ## + ## Don't unwrap EFF yet, we need to preserve rows + eff <- read_vcf@info["EFF"] + + stopifnot(nrow(chrom_pos) == nrow(ref_alt_filter)) + stopifnot(nrow(ref_alt_filter) == nrow(dp_af)) + stopifnot(nrow(dp_af) == nrow(eff)) + + ## EFF data contains nested constructs we need to unify all + ## data sources first, and then explode the EFF column. + united <- as_tibble(cbind(chrom_pos, ref_alt_filter, dp_af, eff)) # nolint + united_exploderows <- unnest(united, cols = c(EFF)) # nolint + + united_exploderows <- united_exploderows %>% + dplyr::mutate(CHROM = seqnames, POS = start) %>% + dplyr::select(CHROM, POS, REF, ALT, FILTER, DP, AF, EFF) + + ## EFF columns are defined here: + ## https://pcingola.github.io/SnpEff/se_inputoutput/ + options(warn = -1) ## suppress warnings + seperated_info <- united_exploderows %>% + separate(EFF, sep = "[(|)]", + extra = "merge", ## extra values merged into "extra" column + into = c("EFF[*].EFFECT", "EFF[*].IMPACT", "EFF[*].FUNCLASS", + "codon.change", "EFF[*].AA", "AA.length", + "EFF[*].GENE", "trans.biotype", "gene.coding", + "trans.id", "exon.rank", "gt.num", "warnings", + "extra")) + options(warn = 0) + ## If there is data that has been dropped or filled-in, we will see it in + ## the "extra" column if it isn't NA or an empty quote. + test_missing <- seperated_info %>% + dplyr::select("CHROM", "POS", "extra") %>% + replace_na(list(extra = "")) %>% + filter(extra != "") + + if (nrow(test_missing) > 0) { + print(test_missing) + stop("Extra values were not parsed") + } + + vcf_info <- seperated_info %>% + dplyr::select("CHROM", "POS", "REF", "ALT", "FILTER", "DP", "AF", + "EFF[*].EFFECT", "EFF[*].IMPACT", "EFF[*].FUNCLASS", + "EFF[*].AA", "EFF[*].GENE") %>% + ## now we de-duplicate any rows that arise from subselecting columns + dplyr::distinct() + + ## At this point, we would still have rows which share a POS and ALT pair + ## which could be problematic for the heatmap plot later. + ## + ## This is not something to worry about here, and is resolved in the heatmap + ## script later. + write.table(vcf_info, file = output_tab, + quote = F, sep = "\t", row.names = F) +} + + + # M A I N +stopifnot(exists("samples")) + +for (i in seq_len(nrow(samples))) { + entry <- samples[i, ]; + if (entry$exts %in% c("vcf", "vcf.gz")) { + in_vcf <- entry$files + out_tsv <- paste0(entry$ids, ".tsv") ## use local dir + tsv_eff_from_vcf(in_vcf, out_tsv) + ## point to the new file + samples[i, ]$files <- out_tsv + message(paste(entry$ids, ": converted from VCF to tabular")) + } else { + message(paste(entry$ids, ": already tabular")) + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpfreqplot.xml Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,311 @@ +<tool id="snpfreqplot" name="Variant Frequency Plot" version="@VERSION@+galaxy@GALAXY_VERSION@" profile="20.09" + license="GPL-3.0-or-later" > + <description>Generates a heatmap of allele frequencies grouped by variant type for SnpEff-annotated SARS-CoV-2 data</description> + <macros> + <token name="@VERSION@">1.0</token> + <token name="@GALAXY_VERSION@">0</token> + </macros> + <requirements> + <requirement type="package" version="4.0">r-base</requirement> + <requirement type="package" version="1.0.12">r-pheatmap</requirement> + <requirement type="package" version="1.3.0">r-tidyverse</requirement> + <requirement type="package" version="1.36.0">bioconductor-variantannotation</requirement> + <requirement type="package" version="">xorg-libxt</requirement> + </requirements> + <edam_topics> + <edam_topic>topic_0797</edam_topic> + <edam_topic>topic_0092</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_3436</edam_operation> + </edam_operations> + <command detect_errors="exit_code"><![CDATA[ +#set $outfile = "tmp_output." + str($advanced.output_type) + +cat '$__tool_directory__/helperFunctions.R' > /dev/null +&& cat '$__tool_directory__/snpEffExtract.R' > /dev/null +&& cat '$__tool_directory__/heatmap_for_variants.R' > /dev/null +&& echo "output file: $outfile" +&& Rscript '$configscript' + ]]> + </command> + <configfiles> + <configfile name="configscript"><![CDATA[ +## 1. Set Sample Inputs +## ------------------ +## Create a dataframe of sample ids, filetypes, and filenames +## from the input collection. At this point, the list could be +## of mixed type (vcf and tabular), though maybe Galaxy +## restricts that. +samples = list(ids = c(), exts= c(), files = c()) +#for $i, $file in enumerate($sinputs): +samples\$ids = c(samples\$ids, '${file.element_identifier}') +samples\$exts = c(samples\$exts, '${file.extension}') +samples\$files = c(samples\$files, '${file}') +#end for +samples = data.frame(samples, stringsAsFactors=F) + +## 2. Input Conversion (external script) +## ---------------------------------- +## We source the input conversion script *after* the samples +## have been populated, so that it performs an inplace replacement +## of the vcf inputs with their converted tabular counterparts. +## +## All samples are all tabular after this point +source('$__tool_directory__/helperFunctions.R') +source('$__tool_directory__/snpEffExtract.R') + +## 3. Galaxy Params +## -------------- +## Set the general script parameters from the UI +variant_frequency <- as.numeric( '$varfreq' ) +brewer_color_gene_annotation <- as.character( '$advanced.color' ) + +#if str($clustering.do) == "TRUE": +pheat_clustering <- TRUE +pheat_clustering_method <- as.character( '$clustering.method' ) +pheat_number_of_clusters <- as.integer( '$clustering.nclust' ) +#else +pheat_clustering <- FALSE +pheat_clustering_method <- "ward.D2" +pheat_number_of_clusters <- 5 +#end if + +ratio = as.numeric('$advanced.ratio') +out_ext = '$advanced.output_type' +out_file = paste0("tmp_output.", out_ext) + +## 4. Generate Heatmap (external script) +## ---------------------------------- +source('$__tool_directory__/heatmap_for_variants.R') + +]]> + </configfile> + </configfiles> + <inputs> + <param name="sinputs" format="tabular,vcf" type="data" multiple="true" + collection_type="list" label="Variant lists data" + help="Select at least two datasets (or a dataset collection) with variant lists (see the tool help below for format details). Datasets are expected to represent individual samples and dataset names will be used as sample identifiers." /> + <param name="varfreq" type="float" min="0" max="1" value="0.1" + label="Variant Frequency Threshold" + help="Only plot variants with an intrasample frequency above this threshold in at least one sample." /> + <section name="advanced" title="Image Properties" expanded="true"> + <param name="output_type" type="select" label="Plot output format" > + <option value="pdf" selected="true" >PDF</option> + <option value="png" >PNG</option> + <option value="svg">SVG</option> + <option value="tiff" >TIFF</option> + <option value="bmp" >BMP</option> + <option value="jpeg" >JPEG</option> + </param> + <param name="ratio" label="Cell Ratio" type="float" + min="0.05" value="0.67" max="20" + help="Width:Height ratio of individual heatmap cells" /> + <param name="color" type="select" label="Color palette used for the gene annotations" > + <option value="Set1" /> + <option value="Set2" /> + <option value="Set3" selected="true" /> + <option value="Pastel2" /> + <option value="Pastel1" /> + <option value="Paired" /> + <option value="Dark2" /> + <option value="Accent" /> + <option value="YlOrRd" /> + <option value="YlOrBr" /> + <option value="YlGnBu" /> + <option value="YlGn" /> + <option value="Reds" /> + <option value="RdPu" /> + <option value="Purples" /> + <option value="PuRd" /> + <option value="PuBuGn" /> + <option value="PuBu" /> + <option value="OrRd" /> + <option value="Oranges" /> + <option value="Greys" /> + <option value="Greens" /> + <option value="GnBu" /> + <option value="BuPu" /> + <option value="BuGn" /> + <option value="Blues" /> + <option value="Spectral" /> + <option value="RdYlGn" /> + <option value="RdYlBu" /> + <option value="RdGy" /> + <option value="RdBu" /> + <option value="PuOr" /> + <option value="PRGn" /> + <option value="PiYG" /> + <option value="BrBG" /> + </param> + </section> + <conditional name="clustering"> + <param name="do" type="select" label="Perform Clustering?" > + <option value="TRUE">Yes</option> + <option value="FALSE" selected="true">No</option> + </param> + <when value="TRUE" > + <param name="nclust" type="integer" + min="1" value="1" label="Number of clusters" /> + <param name="method" type="select" label="Clustering method" > + <option value="ward.D" /> + <option value="ward.D2" selected="true" /> + <option value="single" /> + <option value="complete" /> + <option value="average" >average (UPGMA)</option> + <option value="mcquitty" >mcquitty (WPGMA)</option> + <option value="median" >median (WPGMC)</option> + <option value="centroid" >centroid (UPGMC)</option> + </param> + </when> + <when value="FALSE" /> + </conditional> + </inputs> + <outputs> + <data name="outfile" format="pdf" from_work_dir="tmp_output.*" + label="Variant-Frequency Plot on ${on_string}: ${advanced.output_type}"> + <change_format> + <when input="advanced.output_type" value="svg" format="svg" /> + <when input="advanced.output_type" value="png" format="png" /> + <when input="advanced.output_type" value="tiff" format="tiff" /> + <when input="advanced.output_type" value="bmp" format="bmp" /> + <when input="advanced.output_type" value="jpeg" format="jpg" /> + </change_format> + </data> + </outputs> + <tests> + <test expect_num_outputs="1"> + <!-- PDF, tabular inputs --> + <param name="sinputs" ftype="tabular" value="input436.tabular,input437.tabular,input438.tabular,input439.tabular,input440.tabular,input441.tabular,input442.tabular,input443.tabular,input444.tabular" /> + <output name="outfile" ftype="pdf" value="heatmap.default.pdf" compare="sim_size" delta="250" /> + </test> + <test expect_num_outputs="1"> + <!-- PNG, multiple inputs, non-numeric IDS --> + <param name="sinputs" ftype="tabular" value="input436.tabular,input437.tabular,input443.tabular,input444.tabular" /> + <param name="varfreq" value="0.5" /> + <section name="advanced" > + <param name="color" value="Spectral" /> + <param name="output_type" value="png" /> + </section> + <output name="outfile" ftype="png" value="heatmap.imageopts.png" compare="sim_size" delta="86000" /> + </test> + <test expect_num_outputs="1"> + <!-- SVG, clustering defaults --> + <param name="sinputs" ftype="tabular" value="input438.tabular,input439.tabular,input440.tabular,input441.tabular,input442.tabular" /> + <conditional name="clustering"> + <param name="do" value="TRUE" /> + </conditional> + <section name="advanced" > + <param name="color" value="Greys" /> + <param name="ratio" value="0.8" /> + <param name="output_type" value="svg" /> + </section> + <output name="outfile" ftype="svg"> + <assert_contents> + <has_text text="viewBox="0 0 1156 335"" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <!-- JPEG, clustering extras, mixed alphanumeric labels --> + <param name="sinputs" ftype="tabular" value="input436.tabular,input443.tabular,input438.tabular,input444.tabular" /> + <conditional name="clustering"> + <param name="do" value="TRUE" /> + <param name="nclust" value="2" /> + <param name="method" value="centroid" /> + </conditional> + <section name="advanced" > + <param name="color" value="Purples" /> + <param name="ratio" value="1.2" /> + <param name="output_type" value="jpeg" /> + </section> + <output name="outfile" ftype="jpg" value="heatmap.clustering2.jpeg" compare="sim_size" delta="121000" /> + </test> + <test expect_num_outputs="1"> + <!-- PDF, vcf test --> + <param name="sinputs" ftype="vcf" value="snpeff.123.vcf,snpeff.456.vcf,snpeff.789.vcf" /> + <section name="advanced" > + <param name="color" value="PuBuGn" /> + <param name="output_type" value="pdf" /> + </section> + <output name="outfile" ftype="pdf" value="heatmap.from_vcf.pdf" compare="sim_size" delta="250" /> + </test> + <test expect_num_outputs="1"> + <!-- SVG, problematic vcf test --> + <param name="sinputs" ftype="vcf" value="1084592.vcf,1085080.vcf,1085445.vcf,1085841.vcf,1085990.vcf" /> + <section name="advanced" > + <param name="output_type" value="svg" /> + </section> + <output name="outfile" ftype="svg"> + <assert_contents> + <has_text text="viewBox="0 0 754 271"" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <!-- SVG, Vcf test with problematic splice+syn at snpeff789.vcf for threshold = 0.0222 --> + <param name="sinputs" ftype="vcf" value="snpeff.123.vcf,snpeff.456.vcf,snpeff.789.vcf" /> + <param name="varfreq" value="0.0222" /> + <section name="advanced" > + <param name="output_type" value="svg" /> + </section> + <output name="outfile" ftype="svg"> + <assert_contents> + <has_text text="viewBox="0 0 3101 697"" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**What it does** + +This tool generates multi-sample variant-frequency plots from SnpEff-annotated +viral variant lists with optional hierarchical clustering of the samples. + +.. class:: Warning mark + + Currently, this tool has been tested only on SARS-CoV-2 variant data. + While the intention is to have it work for viral variant data in general, + be prepared for unexpected behavior with other input data at the current + development stage. + +---- + +The tool expects input variant lists in one of the following two formats: + +1. VCF datasets as produced by standard variant callers with + + - variant allele frequencies encoded in an ``AF`` INFO field + - variant functional genomic effects annotated using SnpEff's EFF format (SnpEff's ANN format is not currently supported!) + +2. tabular datasets with columns listing, at least, the following variant properties: + + - ``CHROM`` + - ``POS`` + - ``REF`` + - ``ALT`` + - ``AF`` + - ``EFF[*].AA`` + - ``EFF[*].GENE`` + - ``EFF[*].EFFECT`` + + Such files can be produced with SnpSift Extract Fields and can be useful if + preprocessing of the lists with standard text processing tools is required. + +---- + +Example output: + +.. image:: /static/images/example_output.png + + ]]></help> + <citations> + <citation type="bibtex">@unpublished{Fuchs2020, + author = {Fuchs, Jonas}, + title = {}, + year = {2020}, + note = {Multi-sample annotated viral variant-frequency plots based on the R pheatmap package.}, + address = {Institute for Virology, University of Freiburg} + }</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1084592.vcf Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,327 @@ +##fileformat=VCFv4.0 +##fileDate=20201106 +##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-14951 -o /data/dnb03/galaxy_db/job_working_directory/012/246/12246258/tmp/lofreq2_call_parallelo8d8yqgo/0.vcf.gz reads.bam +##reference=reference.fa +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> +##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> +##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant)."> +##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> +##FILTER=<ID=min_snvqual_77,Description="Minimum SNV Quality (Phred) 77"> +##FILTER=<ID=min_indelqual_63,Description="Minimum Indel Quality (Phred) 63"> +##FILTER=<ID=min_snvqual_80,Description="Minimum SNV Quality (Phred) 80"> +##FILTER=<ID=min_indelqual_66,Description="Minimum Indel Quality (Phred) 66"> +##FILTER=<ID=min_af_0.050000,Description="Minimum allele frequency 0.050000"> +##FILTER=<ID=min_dp_5,Description="Minimum Coverage 5"> +##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000"> +##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani" +##SnpEffCmd="SnpEff -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -stats /data/dnb03/galaxy_db/job_working_directory/012/246/12246325/outputs/galaxy_dataset_6f0d993e-795a-409c-9e60-c42e81b8063a.dat NC_045512.2 /data/dnb03/galaxy_db/files/6/9/2/dataset_692b463b-8a0c-40e3-8a87-942e48d53fcd.dat " +##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype [ | ERRORS | WARNINGS ] )' "> +##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +#CHROM POS ID REF ALT QUAL FILTER INFO +NC_045512.2 164 . C T 133.0 min_af_0.050000 AF=0.001348;DP=16325;DP4=12679,3617,21,6;SB=0 +NC_045512.2 241 . C T 49314.0 PASS AF=0.990942;DP=5741;DP4=1,0,2961,2774;SB=0 +NC_045512.2 323 . GT G 75.0 min_af_0.050000 AF=0.000602;DP=16624;DP4=3541,13119,3,7;HRUN=4;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||tta/|L21|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L21|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L21|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L21|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 343 . G A 92.0 min_af_0.050000 AF=0.000967;DP=26891;DP4=13149,13701,12,17;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V26|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V26|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V26|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V26|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A) +NC_045512.2 424 . AGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTT A 49314.0 PASS AF=0.867361;DP=12779;DP4=908,822,9479,1605;HRUN=1;SB=1918;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtagaagttgaaaaaggcgttttgcctcaacttgaa/gaa|VEVEKGVLPQLE54E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtagaagttgaaaaaggcgttttgcctcaacttgaa/gaa|VEVEKGVLPQLE54E|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtagaagttgaaaaaggcgttttgcctcaacttgaa/gaa|VEVEKGVLPQLE54E|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtagaagttgaaaaaggcgttttgcctcaacttgaa/gaa|VEVEKGVLPQLE54E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME) +NC_045512.2 457 . T TA 1257.0 min_af_0.050000 AF=0.006406;DP=11239;DP4=9516,1651,67,5;HRUN=1;SB=11;INDEL;EFF=FRAME_SHIFT(HIGH||gaa/Agaa|E65R?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|TA),FRAME_SHIFT(HIGH||gaa/Agaa|E65R?|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|TA|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||gaa/Agaa|E65R?|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|TA|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||gaa/Agaa|E65R?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|TA);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 509 . GGTCATGTTATGGTT G 158.0 min_af_0.050000 AF=0.003328;DP=5709;DP4=3637,2595,8,11;HRUN=2;SB=7;INDEL;EFF=FRAME_SHIFT(HIGH||ggtcatgttatggttgag/|GHVMVE82|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggtcatgttatggttgag/|GHVMVE82|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggtcatgttatggttgag/|GHVMVE82|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggtcatgttatggttgag/|GHVMVE82|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 558 . G T 440.0 min_af_0.050000 AF=0.007488;DP=4941;DP4=2892,2007,24,13;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G98V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G98V|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G98V|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G98V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T) +NC_045512.2 602 . G A 134.0 min_af_0.050000 AF=0.001451;DP=14475;DP4=3277,11172,8,16;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E113K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E113K|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E113K|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E113K|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A) +NC_045512.2 685 . AAAGTCATTT A 186.0 min_af_0.050000 AF=0.001184;DP=14362;DP4=3266,11121,4,13;HRUN=3;SB=0;INDEL;EFF=CODON_DELETION(MODERATE||aagtcattt/|KSF141|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_DELETION(MODERATE||aagtcattt/|KSF141|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_DELETION(MODERATE||aagtcattt/|KSF141|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_DELETION(MODERATE||aagtcattt/|KSF141|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A) +NC_045512.2 951 . A G 160.0 min_af_0.050000 AF=0.003730;DP=4021;DP4=506,3495,0,17;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tGc|Y229C|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tGc|Y229C|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tGc|Y49C|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tGc|Y49C|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1019 . C T 109.0 min_af_0.050000 AF=0.000957;DP=21953;DP4=17831,4091,17,7;SB=7;EFF=STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q252*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q252*|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q72*|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q72*|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04) +NC_045512.2 1020 . A G 108.0 min_af_0.050000 AF=0.000957;DP=21933;DP4=17771,4130,20,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q252R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q252R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q72R|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q72R|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1026 . CT C 166.0 min_af_0.050000 AF=0.000872;DP=21786;DP4=17611,4236,13,6;HRUN=4;SB=6;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F255|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F255|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F75|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F75|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) +NC_045512.2 1027 . T C 192.0 min_af_0.050000 AF=0.001376;DP=21810;DP4=17520,4226,28,6;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P254|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P254|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P74|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P74|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1115 . A T 736.0 min_af_0.050000;sb_fdr AF=0.008634;DP=6370;DP4=2492,3819,4,51;SB=70;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I284F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I284F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I104F|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I104F|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1133 . A T 481.0 min_af_0.050000 AF=0.006411;DP=6551;DP4=2807,3701,35,7;SB=68;EFF=STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K290*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K290*|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K110*|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K110*|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04) +NC_045512.2 1201 . C T 184.0 min_af_0.050000 AF=0.001608;DP=18660;DP4=3443,15178,7,23;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C312|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C312|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C132|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C132|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1211 . T C 100.0 min_af_0.050000 AF=0.001014;DP=18739;DP4=3499,15213,6,15;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C316R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C316R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C136R|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C136R|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1644 . A C 438.0 min_af_0.050000 AF=0.003210;DP=14641;DP4=11631,2951,20,31;SB=94;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N460T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N460T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N280T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N280T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1647 . T A 496.0 min_af_0.050000 AF=0.003406;DP=14679;DP4=11564,3059,19,34;SB=108;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I461N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I461N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I281N|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I281N|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1656 . T A 395.0 min_af_0.050000 AF=0.003129;DP=14702;DP4=11472,3173,20,31;SB=87;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V464D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V464D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V284D|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V284D|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1659 . G T 351.0 min_af_0.050000 AF=0.002908;DP=14789;DP4=11547,3193,16,29;SB=90;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G465V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G465V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G285V|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G285V|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1702 . T C 289.0 min_af_0.050000 AF=0.002467;DP=14590;DP4=11407,3111,29,7;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S479|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S479|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S299|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S299|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1710 . C T 275.0 min_af_0.050000 AF=0.002280;DP=14476;DP4=11396,3040,21,17;SB=29;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A482V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A482V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A302V|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A302V|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1721 . G A 140.0 min_af_0.050000 AF=0.001466;DP=14325;DP4=11313,2989,14,7;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A486T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A486T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A306T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A306T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1868 . G A 132.0 min_af_0.050000 AF=0.001298;DP=16183;DP4=3249,12900,4,20;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A535T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A535T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A355T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A355T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1874 . G A 95.0 min_af_0.050000 AF=0.001055;DP=16116;DP4=3127,12965,3,15;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A537T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A537T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A357T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A357T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1886 . G A 84.0 min_af_0.050000 AF=0.001075;DP=15820;DP4=2886,12908,4,17;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A541T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A541T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A361T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A361T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1914 . G A 137.0 min_af_0.050000 AF=0.001452;DP=15147;DP4=2713,12407,6,18;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R550H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R550H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R370H|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R370H|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 2904 . TA T 78.0 min_af_0.050000 AF=0.001265;DP=6322;DP4=5093,1224,5,3;HRUN=5;SB=7;INDEL;EFF=FRAME_SHIFT(HIGH||act/|T882|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||act/|T882|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||act/|T64|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||act/|T64|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 3036 . TC T 93.0 min_af_0.050000 AF=0.002984;DP=2011;DP4=1107,916,3,3;HRUN=1;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttc/|F924|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),FRAME_SHIFT(HIGH||ttc/|F924|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),FRAME_SHIFT(HIGH||ttc/|F106|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||ttc/|F106|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 3037 . C T 49314.0 PASS AF=0.991580;DP=2019;DP4=0,0,1111,902;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 3259 . G T 128.0 min_af_0.050000 AF=0.002216;DP=6770;DP4=5516,1236,14,1;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q998H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q998H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q180H|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q180H|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 3412 . TA T 76.0 min_af_0.050000 AF=0.001168;DP=6847;DP4=1290,5560,1,7;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K1051|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K1051|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K233|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K233|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 4174 . TA T 155.0 min_af_0.050000 AF=0.000954;DP=19915;DP4=15786,4180,15,4;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K1305|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K1305|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K487|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K487|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 4185 . G T 321.0 min_af_0.050000 AF=0.002271;DP=20253;DP4=15843,4355,24,24;SB=46;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G1307V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G1307V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G489V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G489V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4308 . A G 307.0 min_af_0.050000 AF=0.001970;DP=21317;DP4=4425,16849,9,34;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K1348R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K1348R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K530R|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K530R|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4321 . CT C 96.0 min_af_0.050000 AF=0.000624;DP=20829;DP4=4119,17027,3,10;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||tac/|Y1354|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tac/|Y1354|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tac/|Y536|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tac/|Y536|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 4391 . C T 91.0 min_af_0.050000 AF=0.001118;DP=21462;DP4=4942,16483,5,24;SB=1;EFF=STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R1376*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R1376*|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R558*|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R558*|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04) +NC_045512.2 4412 . GA G 74.0 min_af_0.050000 AF=0.000953;DP=7343;DP4=4106,3237,2,5;HRUN=2;SB=5;INDEL;EFF=FRAME_SHIFT(HIGH||gaa/|E1383|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gaa/|E1383|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gaa/|E565|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gaa/|E565|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 5284 . C T 108.0 min_af_0.050000 AF=0.002361;DP=5082;DP4=3452,1616,2,10;SB=34;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N1673|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N1673|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N855|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N855|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5291 . CT C 298.0 min_af_0.050000 AF=0.002476;DP=8887;DP4=7154,1717,15,7;HRUN=2;SB=7;INDEL;EFF=FRAME_SHIFT(HIGH||ctt/|L1676|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/|L1676|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/|L858|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/|L858|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 5305 . G T 135.0 min_af_0.050000 AF=0.001876;DP=9060;DP4=7211,1817,14,4;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L1680F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L1680F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L862F|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L862F|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5411 . G A 238.0 min_af_0.050000 AF=0.003764;DP=6110;DP4=3843,2238,8,16;SB=23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A1716T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A1716T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A898T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A898T|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5743 . G C 189.0 min_af_0.050000 AF=0.005262;DP=3421;DP4=1740,1660,3,16;SB=26;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1826D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1826D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1008D|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1008D|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5744 . T C 311.0 min_af_0.050000 AF=0.007656;DP=3396;DP4=1744,1626,8,18;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1827H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1827H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1009H|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1009H|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5809 . AGACGGTGCTTTACTT A 92.0 min_af_0.050000 AF=0.000900;DP=9999;DP4=2218,7782,1,8;HRUN=1;SB=1;INDEL;EFF=CODON_DELETION(MODERATE||gacggtgctttactt/|DGALL1849|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_DELETION(MODERATE||gacggtgctttactt/|DGALL1849|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),CODON_DELETION(MODERATE||gacggtgctttactt/|DGALL1031|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),CODON_DELETION(MODERATE||gacggtgctttactt/|DGALL1031|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5924 . G A 89.0 min_af_0.050000 AF=0.000850;DP=23540;DP4=13235,10277,7,14;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1887I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1887I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1069I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1069I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6044 . AATT A 89.0 min_af_0.050000 AF=0.001604;DP=4363;DP4=1797,2576,4,3;HRUN=2;SB=3;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aatttt/att|NF1927I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aatttt/att|NF1927I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aatttt/att|NF1109I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aatttt/att|NF1109I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6139 . AT A 118.0 min_af_0.050000 AF=0.000973;DP=14384;DP4=2789,11592,3,11;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttc/|F1960|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttc/|F1960|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttc/|F1142|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttc/|F1142|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 6177 . AT A 194.0 min_af_0.050000 AF=0.001019;DP=18642;DP4=2648,15985,2,17;HRUN=2;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||tat/|Y1972|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tat/|Y1972|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tat/|Y1154|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tat/|Y1154|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 6179 . TA T 68.0 min_af_0.050000 AF=0.000477;DP=18879;DP4=2626,16309,0,9;HRUN=1;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||tat/|Y1972|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),FRAME_SHIFT(HIGH||tat/|Y1972|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),FRAME_SHIFT(HIGH||tat/|Y1154|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||tat/|Y1154|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 6199 . T C 159.0 min_af_0.050000 AF=0.001119;DP=49166;DP4=31656,17424,42,17;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1978|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1978|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1160|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1160|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6242 . C T 150.0 min_af_0.050000 AF=0.000761;DP=51238;DP4=31718,19455,32,17;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1993Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1993Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1175Y|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1175Y|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6254 . G A 127.0 min_af_0.050000 AF=0.000758;DP=39566;DP4=31533,7989,26,8;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1997T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1997T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1179T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1179T|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6270 . C T 81.0 min_af_0.050000 AF=0.000632;DP=39548;DP4=30669,8836,22,9;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T2002M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T2002M|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1184M|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1184M|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6271 . G A 176.0 min_af_0.050000 AF=0.001023;DP=39089;DP4=30156,8871,25,21;SB=32;EFF=SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T2002|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T2002|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1184|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1184|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6297 . G A 180.0 min_af_0.050000 AF=0.000958;DP=38631;DP4=29557,9033,26,11;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R2011H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R2011H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R1193H|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R1193H|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6312 . CA C 294.0 min_af_0.050000 AF=0.000902;DP=37682;DP4=29256,8543,26,8;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K2017|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K2017|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1199|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1199|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 6396 . T C 258.0 min_af_0.050000 AF=0.002203;DP=14981;DP4=6634,8302,5,31;SB=38;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L2044P|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L2044P|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L1226P|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L1226P|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6409 . T C 102.0 min_af_0.050000 AF=0.000752;DP=34578;DP4=6634,27908,5,23;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S2048|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S2048|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1230|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1230|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6503 . G A 102.0 min_af_0.050000 AF=0.000761;DP=31528;DP4=5228,26256,5,25;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A2080T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A2080T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1262T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1262T|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6513 . G T 199.0 min_af_0.050000 AF=0.001168;DP=30810;DP4=4748,25994,7,49;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aTt|S2083I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aTt|S2083I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aTt|S1265I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aTt|S1265I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6906 . C T 41177.0 PASS AF=0.995383;DP=1083;DP4=1,0,564,518;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2214L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2214L|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S1396L|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S1396L|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 7246 . GT G 95.0 min_af_0.050000 AF=0.005029;DP=1193;DP4=555,642,3,3;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttg/|L2329|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L2329|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L1511|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L1511|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 7614 . G C 134.0 min_af_0.050000 AF=0.010056;DP=895;DP4=349,535,6,3;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W2450S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W2450S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W1632S|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W1632S|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 7615 . G C 135.0 min_af_0.050000 AF=0.010045;DP=896;DP4=350,535,6,3;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgG/tgC|W2450C|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgG/tgC|W2450C|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgG/tgC|W1632C|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgG/tgC|W1632C|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 7772 . CT C 79.0 min_af_0.050000 AF=0.000827;DP=9676;DP4=7597,2126,5,3;HRUN=3;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||tac/|Y2504|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tac/|Y2504|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tac/|Y1686|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tac/|Y1686|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 7788 . C A 130.0 min_af_0.050000 AF=0.003436;DP=3784;DP4=1622,2148,11,2;SB=24;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gAt|A2508D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gAt|A2508D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gAt|A1690D|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gAt|A1690D|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 7813 . TTC T 77.0 min_af_0.050000 AF=0.001577;DP=3805;DP4=1781,2043,3,3;HRUN=2;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||tctcat/|SH2519|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tctcat/|SH2519|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tctcat/|SH1701|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tctcat/|SH1701|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 7889 . GT G 703.0 min_af_0.050000 AF=0.004789;DP=10024;DP4=2088,7910,10,38;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F2543|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F2543|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F1725|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F1725|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 7911 . G C 105.0 min_af_0.050000 AF=0.001495;DP=10036;DP4=2129,7889,2,13;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C2549S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C2549S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C1731S|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C1731S|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 8017 . G A 112.0 min_af_0.050000 AF=0.002980;DP=5034;DP4=4162,854,8,7;SB=21;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A2584|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A2584|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A1766|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A1766|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 8387 . A C 82.0 min_af_0.050000 AF=0.003079;DP=3897;DP4=3112,767,8,5;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Cac|N2708H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Cac|N2708H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Cac|N1890H|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Cac|N1890H|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 8937 . C T 98.0 min_af_0.050000 AF=0.001505;DP=9303;DP4=7370,1913,10,4;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A2891V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A2891V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A128V|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A128V|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 8991 . C T 141.0 min_af_0.050000 AF=0.001933;DP=9310;DP4=7384,1900,17,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A2909V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A2909V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A146V|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A146V|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 9593 . T C 83.0 min_af_0.050000 AF=0.001116;DP=12543;DP4=9868,2657,13,3;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L3110|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L3110|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L347|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L347|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 9656 . A G 276.0 min_af_0.050000;sb_fdr AF=0.005870;DP=3918;DP4=1706,2185,22,1;SB=67;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M3131V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M3131V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M368V|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M368V|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 9807 . G A 135.0 min_af_0.050000 AF=0.001628;DP=11669;DP4=2191,9457,4,15;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C3181Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C3181Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C418Y|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C418Y|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 9808 . C T 149.0 min_af_0.050000 AF=0.001800;DP=11666;DP4=2188,9439,6,31;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C3181|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C3181|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C418|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C418|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 10450 . C T 569.0 min_af_0.050000 AF=0.010680;DP=3839;DP4=2984,812,31,10;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P3395|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P3395|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P132|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P132|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 10481 . G A 110.0 min_af_0.050000 AF=0.003086;DP=3564;DP4=2636,916,11,1;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G3406S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G3406S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G143S|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G143S|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 10615 . C T 122.0 min_af_0.050000 AF=0.003522;DP=3407;DP4=1050,2343,7,6;SB=8;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3450|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3450|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D187|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D187|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 10679 . T C 451.0 min_af_0.050000 AF=0.010126;DP=3259;DP4=866,2359,7,26;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y3472H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y3472H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y209H|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y209H|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11083 . G T 248.0 min_af_0.050000 AF=0.002203;DP=17707;DP4=13818,3821,39,10;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L3606F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L3606F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L37F|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L37F|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11095 . CT C 240.0 min_af_0.050000 AF=0.001401;DP=17844;DP4=13909,3979,18,7;HRUN=5;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||tta/|L3612|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L3612|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L43|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L43|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 11104 . T C 146.0 min_af_0.050000 AF=0.001454;DP=17883;DP4=13846,3990,25,4;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P3613|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P3613|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P44|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P44|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11139 . C T 105.0 min_af_0.050000 AF=0.001114;DP=17949;DP4=13766,4153,16,6;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A3625V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A3625V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A56V|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A56V|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11248 . G A 90.0 min_af_0.050000 AF=0.001085;DP=17516;DP4=3720,13767,7,17;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M3661I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M3661I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M92I|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M92I|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11321 . G A 115.0 min_af_0.050000 AF=0.001101;DP=19067;DP4=3969,15072,6,17;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A3686T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A3686T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A117T|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A117T|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11354 . G A 145.0 min_af_0.050000 AF=0.001076;DP=25103;DP4=9900,15171,11,18;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A3697T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A3697T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A128T|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A128T|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11406 . T G 80.0 min_af_0.050000 AF=0.001365;DP=8792;DP4=6687,2087,7,7;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gGc|V3714G|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gGc|V3714G|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gGc|V145G|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gGc|V145G|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11540 . GT G 98.0 min_af_0.050000 AF=0.001671;DP=5387;DP4=1684,3719,5,4;HRUN=5;SB=8;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F3760|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F3760|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F191|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F191|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 11654 . T C 120.0 min_af_0.050000 AF=0.001515;DP=13857;DP4=6675,7149,9,13;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F3797L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F3797L|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F228L|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F228L|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11939 . G A 81.0 min_af_0.050000 AF=0.000866;DP=19641;DP4=16008,3601,13,6;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V3892I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V3892I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V33I|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V33I|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11952 . A T 80.0 min_af_0.050000 AF=0.000943;DP=19088;DP4=15213,3849,13,6;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aTt|N3896I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aTt|N3896I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aTt|N37I|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aTt|N37I|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12128 . G A 91.0 min_af_0.050000 AF=0.000925;DP=20531;DP4=4035,16468,3,20;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A3955T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A3955T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A13T|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A13T|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12129 . C T 87.0 min_af_0.050000 AF=0.000876;DP=20539;DP4=4021,16498,3,15;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A3955V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A3955V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A13V|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A13V|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12141 . C T 93.0 min_af_0.050000 AF=0.000878;DP=21647;DP4=5102,16508,3,16;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3959I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3959I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T17I|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T17I|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12161 . C T 92.0 min_af_0.050000 AF=0.000874;DP=21732;DP4=5048,16660,6,15;SB=2;EFF=STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q3966*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q3966*|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q24*|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q24*|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04) +NC_045512.2 12164 . G T 351.0 min_af_0.050000 AF=0.002070;DP=21735;DP4=5033,16647,15,33;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A3967S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A3967S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A25S|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A25S|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12201 . A G 204.0 min_af_0.050000 AF=0.001584;DP=20834;DP4=4220,16578,7,29;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K3979R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K3979R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K37R|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K37R|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12224 . G A 103.0 min_af_0.050000 AF=0.000998;DP=20040;DP4=3616,16391,5,18;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3987T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3987T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A45T|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A45T|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12458 . A G 322.0 min_af_0.050000 AF=0.002236;DP=17442;DP4=13770,3621,34,6;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T4065A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T4065A|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T123A|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T123A|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12513 . C T 139.0 min_af_0.050000 AF=0.001298;DP=17726;DP4=13800,3892,14,9;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T4083M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T4083M|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T141M|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T141M|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12578 . G T 99.0 min_af_0.050000 AF=0.002130;DP=6103;DP4=2421,3667,9,5;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D4105Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D4105Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D163Y|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D163Y|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12754 . C T 193.0 min_af_0.050000 AF=0.001165;DP=29183;DP4=14327,14756,21,71;SB=65;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C4163|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C4163|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C23|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C23|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12999 . G A 88.0 min_af_0.050000 AF=0.000980;DP=17347;DP4=4073,13246,5,14;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S4245N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S4245N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S105N|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S105N|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13034 . G A 201.0 min_af_0.050000 AF=0.000910;DP=47277;DP4=29099,18123,31,13;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4257T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4257T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13048 . T C 135.0 min_af_0.050000 AF=0.000711;DP=47843;DP4=29048,18629,26,114;SB=238;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4261|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4261|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P8|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P8|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13049 . G A 162.0 min_af_0.050000 AF=0.000791;DP=48027;DP4=29118,18852,25,20;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4262T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4262T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A9T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A9T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13050 . C T 185.0 min_af_0.050000 AF=0.000853;DP=48077;DP4=29117,18902,27,20;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A4262V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A4262V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A9V|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A9V|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13059 . C T 119.0 min_af_0.050000 AF=0.000665;DP=48140;DP4=28964,19130,18,19;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T4265I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T4265I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T12I|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T12I|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13061 . G A 149.0 min_af_0.050000 AF=0.000747;DP=48218;DP4=28907,19226,43,19;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V4266I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V4266I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V13I|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V13I|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13084 . T C 155.0 min_af_0.050000 AF=0.000894;DP=35812;DP4=28538,7231,27,8;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4273|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4273|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A20|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A20|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13094 . G A 91.0 min_af_0.050000 AF=0.000756;DP=35712;DP4=27866,7809,23,7;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A4277T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A4277T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A24T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A24T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13123 . TG T 284.0 min_af_0.050000 AF=0.001022;DP=34241;DP4=26326,7960,28,7;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||gga/|G4288|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G4288|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G35|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G35|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) +NC_045512.2 13129 . A G 311.0 min_af_0.050000 AF=0.001594;DP=34502;DP4=26344,8069,53,15;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13201 . G T 11905.0 min_af_0.050000 AF=0.045618;DP=13043;DP4=6344,6083,306,296;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P4312|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P4312|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P59|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P59|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13235 . G A 191.0 min_af_0.050000 AF=0.001363;DP=30081;DP4=7582,22442,11,32;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4324T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4324T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A71T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A71T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13254 . G A 125.0 min_af_0.050000 AF=0.000926;DP=34575;DP4=8035,26482,10,29;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C4330Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C4330Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C77Y|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C77Y|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13260 . G A 110.0 min_af_0.050000 AF=0.000832;DP=34837;DP4=8162,26632,9,26;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C4332Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C4332Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C79Y|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C79Y|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13299 . TA T 141.0 min_af_0.050000 AF=0.000576;DP=34699;DP4=8173,26639,4,16;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K4346|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K4346|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K93|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K93|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) +NC_045512.2 13334 . G A 93.0 min_af_0.050000 AF=0.000719;DP=33393;DP4=6325,27020,8,20;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A4357T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A4357T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A104T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A104T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13345 . T C 142.0 min_af_0.050000 AF=0.000923;DP=37923;DP4=11024,26838,17,19;SB=15;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4360|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4360|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P107|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P107|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13350 . GT G 67.0 min_af_0.050000 AF=0.000345;DP=37715;DP4=10940,26835,4,9;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F4363|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F4363|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F110|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F110|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) +NC_045512.2 13373 . TG T 74.0 min_af_0.050000 AF=0.000556;DP=16174;DP4=9855,6326,3,6;HRUN=1;SB=7;INDEL;EFF=FRAME_SHIFT(HIGH||tgt/|C4370|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),FRAME_SHIFT(HIGH||tgt/|C4370|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),FRAME_SHIFT(HIGH||tgt/|C117|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||tgt/|C117|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.11) +NC_045512.2 13451 . G A 139.0 min_af_0.050000 AF=0.002377;DP=6732;DP4=5314,1401,11,5;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4396T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4396T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|12|ORF1ab|protein_coding|CODING|YP_009725312.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13565 . T G 126.0 min_af_0.050000 AF=0.002191;DP=6845;DP4=1460,5365,11,6;SB=38;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gGa|V4434G|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gGa|V42G|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13571 . G T 626.0 min_af_0.050000 AF=0.007100;DP=6901;DP4=1486,5364,11,39;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G4436V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G44V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13616 . A G 107.0 min_af_0.050000 AF=0.001711;DP=10521;DP4=1399,9100,2,17;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K4451R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K59R|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13836 . G A 153.0 min_af_0.050000 AF=0.000927;DP=34520;DP4=6715,27756,10,24;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R4524|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R132|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13966 . G A 87.0 min_af_0.050000 AF=0.001010;DP=15845;DP4=13708,2113,14,3;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4568T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A176T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13982 . G A 361.0 min_af_0.050000 AF=0.003139;DP=13381;DP4=10986,2346,23,20;SB=49;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R4573H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R181H|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13988 . G A 99.0 min_af_0.050000 AF=0.001272;DP=12581;DP4=10082,2474,15,2;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R4575H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R183H|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14408 . C T 33427.0 PASS AF=0.987778;DP=900;DP4=0,3,371,524;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4715L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P323L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14624 . G A 100.0 min_af_0.050000 AF=0.001576;DP=8885;DP4=6982,1886,13,3;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C4787Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C395Y|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14653 . G T 110.0 min_af_0.050000 AF=0.001667;DP=8999;DP4=6980,2002,13,3;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ttt|V4797F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ttt|V405F|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14848 . CTATTTG C 71.0 min_af_0.050000 AF=0.000856;DP=8180;DP4=1608,6620,1,6;HRUN=1;SB=0;INDEL;EFF=CODON_DELETION(MODERATE||tttgta/|FV4863|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||tttgta/|FV471|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME) +NC_045512.2 15016 . G T 479.0 min_af_0.050000 AF=0.014688;DP=2451;DP4=1905,509,26,10;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Tca|A4918S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Tca|A526S|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15128 . G A 80.0 min_af_0.050000 AF=0.003114;DP=2890;DP4=662,2204,3,10;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C4955Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C563Y|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15157 . CA C 88.0 min_af_0.050000 AF=0.002424;DP=2888;DP4=652,2250,1,6;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K4966|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K574|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 15279 . C T 202.0 min_af_0.050000 AF=0.002300;DP=10437;DP4=8333,2073,23,6;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H5005|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H613|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15324 . C T 49314.0 PASS AF=0.989112;DP=8817;DP4=1,1,6751,2058;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N5020|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N628|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15587 . C T 109.0 min_af_0.050000 AF=0.000895;DP=27936;DP4=22151,5748,24,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A5108V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A716V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15602 . G A 148.0 min_af_0.050000 AF=0.001137;DP=28150;DP4=22229,5881,25,8;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R5113H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R721H|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15610 . C T 81.0 min_af_0.050000 AF=0.000720;DP=27789;DP4=22076,5684,17,5;SB=1;EFF=STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q5116*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q724*|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15628 . T C 97.0 min_af_0.050000 AF=0.000810;DP=27146;DP4=21748,5352,23,2;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C5122R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C730R|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15673 . T G 138.0 min_af_0.050000;sb_fdr AF=0.002916;DP=9601;DP4=4640,4919,28,2;SB=65;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Gtt|F5137V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Gtt|F745V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15682 . T A 3086.0 min_af_0.050000 AF=0.019651;DP=9567;DP4=4771,4605,113,78;SB=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y5140N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y748N|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15685 . T A 3070.0 min_af_0.050000 AF=0.019492;DP=9645;DP4=4821,4634,112,78;SB=14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L5141M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L749M|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15752 . C T 130.0 min_af_0.050000 AF=0.000956;DP=27194;DP4=5580,21576,5,26;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A5163V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A771V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15761 . G C 111.0 min_af_0.050000 AF=0.000914;DP=27359;DP4=5595,21715,7,21;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G5166A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G774A|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15784 . T TGAC 140.0 min_af_0.050000 AF=0.000612;DP=27777;DP4=5858,22028,5,12;HRUN=3;SB=4;INDEL;EFF=STOP_GAINED+CODON_CHANGE_PLUS_CODON_INSERTION(HIGH||ttt/tGACtt|F5174*L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|TGAC),STOP_GAINED+CODON_CHANGE_PLUS_CODON_INSERTION(HIGH||ttt/tGACtt|F782*L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|TGAC|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15788 . AGTC A 140.0 min_af_0.050000 AF=0.000617;DP=27575;DP4=5626,21971,5,12;HRUN=1;SB=4;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aagtca/aaa|KS5175K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aagtca/aaa|KS783K|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15959 . C G 86.0 min_af_0.050000 AF=0.001104;DP=16300;DP4=12597,3665,14,5;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gGc|A5232G|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gGc|A840G|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 16073 . C T 104.0 min_af_0.050000 AF=0.001226;DP=15503;DP4=3133,12344,4,17;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A5270V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A878V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 16386 . C T 95.0 min_af_0.050000 AF=0.006667;DP=1050;DP4=288,752,3,4;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C5374|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C50|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 16800 . TA T 143.0 min_af_0.050000 AF=0.001533;DP=9133;DP4=7069,2052,12,2;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||aac/|N5514|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aac/|N190|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 16949 . C T 101.0 min_af_0.050000 AF=0.003001;DP=3665;DP4=1707,1944,5,7;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P5562L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P238L|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 17035 . G A 90.0 min_af_0.050000 AF=0.001462;DP=8890;DP4=2031,6845,4,9;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A5591T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A267T|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 17140 . G A 85.0 min_af_0.050000 AF=0.001241;DP=12090;DP4=9631,2440,12,4;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A5626T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A302T|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 17144 . G A 117.0 min_af_0.050000 AF=0.001660;DP=12046;DP4=9540,2484,14,6;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R5627H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R303H|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 17200 . TTAAAA T 188.0 min_af_0.050000 AF=0.001439;DP=11115;DP4=8773,2405,10,6;HRUN=2;SB=8;INDEL;EFF=FRAME_SHIFT(HIGH||aaatat/|KY5647|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaatat/|KY323|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 17339 . C T 81.0 min_af_0.050000 AF=0.001134;DP=12349;DP4=3036,9291,3,11;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A5692V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A368V|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 17808 . G T 151.0 min_af_0.050000 AF=0.009872;DP=1013;DP4=826,177,9,1;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K5848N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K524N|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 18641 . T A 530.0 min_af_0.050000 AF=0.003382;DP=15673;DP4=11486,4127,27,27;SB=35;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aAa|I6126K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aAa|I201K|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 18687 . CT C 156.0 min_af_0.050000 AF=0.001118;DP=14308;DP4=11344,2973,10,6;HRUN=4;SB=9;INDEL;EFF=FRAME_SHIFT(HIGH||tcc/|S6143|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tcc/|S218|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 18715 . T C 109.0 min_af_0.050000 AF=0.001262;DP=14258;DP4=11215,3019,14,6;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C6151R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C226R|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 18736 . TTTGA T 79.0 min_af_0.050000 AF=0.000635;DP=14178;DP4=11228,2983,7,2;HRUN=3;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||gattac/|DY6159|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gattac/|DY234|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 19172 . C T 142.0 min_af_0.050000 AF=0.001388;DP=15855;DP4=3216,12613,7,16;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T6303I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T378I|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19188 . AT A 219.0 min_af_0.050000 AF=0.001329;DP=15807;DP4=3164,12631,6,15;HRUN=4;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||tgg/|W6310|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgg/|W385|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 19199 . G A 96.0 min_af_0.050000 AF=0.001074;DP=15832;DP4=3167,12645,6,13;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C6312Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C387Y|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19452 . T A 120.0 min_af_0.050000 AF=0.030612;DP=196;DP4=112,78,1,5;SB=10;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcA|A6396|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcA|A471|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19468 . T A 100.0 min_af_0.050000 AF=0.013605;DP=441;DP4=123,312,3,3;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Agc|C6402S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Agc|C477S|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19679 . G T 305.0 min_af_0.050000 AF=0.002634;DP=14427;DP4=11435,2935,30,8;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G6472V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G20V|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19821 . A G 97.0 min_af_0.050000 AF=0.001163;DP=13752;DP4=2628,11106,4,12;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P6519|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P67|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19870 . G A 130.0 min_af_0.050000 AF=0.001286;DP=16326;DP4=4782,11514,9,15;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V6536M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V84M|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 20317 . G T 81.0 min_af_0.050000 AF=0.006459;DP=929;DP4=629,294,5,1;SB=1;EFF=STOP_GAINED(HIGH|NONSENSE|Gaa/Taa|E6685*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),STOP_GAINED(HIGH|NONSENSE|Gaa/Taa|E233*|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 20839 . G A 95.0 min_af_0.050000 AF=0.000824;DP=25489;DP4=12509,12947,18,8;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V6859I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V61I|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 20926 . C T 100.0 min_af_0.050000 AF=0.001257;DP=13527;DP4=10536,2964,13,8;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P6888S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P90S|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 21054 . C T 135.0 min_af_0.050000 AF=0.001728;DP=12156;DP4=2309,9817,5,20;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y6930|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y132|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 21066 . TA T 181.0 min_af_0.050000 AF=0.001502;DP=11985;DP4=2225,9771,3,15;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aat/|N6936|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aat/|N138|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.04) +NC_045512.2 21634 . A AC 95.0 min_af_0.050000 AF=0.003008;DP=2327;DP4=624,1696,2,5;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||cct/ccCt|P26P?|1273|S|protein_coding|CODING|GU280_gp02|1|AC|INFO_REALIGN_3_PRIME) +NC_045512.2 22573 . T C 83.0 min_af_0.050000 AF=0.001085;DP=13831;DP4=11344,2466,18,2;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P337|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 22583 . GT G 209.0 min_af_0.050000 AF=0.001487;DP=14121;DP4=11424,2680,17,4;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F342|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 22591 . C T 138.0 min_af_0.050000 AF=0.001470;DP=14282;DP4=11424,2830,18,7;SB=5;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N343|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 22639 . C T 94.0 min_af_0.050000 AF=0.001122;DP=14257;DP4=11431,2802,13,4;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S359|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 22643 . T A 465.0 min_af_0.050000 AF=0.003306;DP=14216;DP4=11344,2812,33,14;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C361S|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 22644 . G C 442.0 min_af_0.050000 AF=0.003220;DP=14284;DP4=11347,2879,32,14;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C361S|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 22645 . T A 374.0 min_af_0.050000 AF=0.003012;DP=14276;DP4=11332,2884,35,14;SB=8;EFF=STOP_GAINED(HIGH|NONSENSE|tgT/tgA|C361*|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 22852 . A G 87.0 min_af_0.050000 AF=0.001083;DP=13851;DP4=3408,10413,2,15;SB=5;EFF=SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T430|1273|S|protein_coding|CODING|GU280_gp02|1|G) +NC_045512.2 22899 . G T 187.0 min_af_0.050000 AF=0.004985;DP=3410;DP4=2519,874,10,7;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G446V|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 22900 . T A 595.0 min_af_0.050000 AF=0.012915;DP=3252;DP4=2361,843,7,37;SB=145;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggT/ggA|G446|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 23132 . GT G 293.0 min_af_0.050000 AF=0.004197;DP=4289;DP4=758,3519,3,15;HRUN=3;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||tgt/|C525|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 23202 . C T 84.0 min_af_0.050000 AF=0.000879;DP=19331;DP4=14178,5113,15,7;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T547I|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 23209 . A G 118.0 min_af_0.050000 AF=0.001076;DP=19518;DP4=14128,5360,16,7;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T549|1273|S|protein_coding|CODING|GU280_gp02|1|G) +NC_045512.2 23389 . T C 89.0 min_af_0.050000 AF=0.000975;DP=17437;DP4=3751,13662,3,14;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A609|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 23403 . A G 49314.0 PASS AF=0.991866;DP=17334;DP4=2,4,3724,13599;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G) +NC_045512.2 23412 . G A 80.0 min_af_0.050000 AF=0.000918;DP=17437;DP4=3771,13642,2,16;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C617Y|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 23417 . G T 181.0 min_af_0.050000 AF=0.001558;DP=17328;DP4=3727,13562,4,24;SB=3;EFF=STOP_GAINED(HIGH|NONSENSE|Gaa/Taa|E619*|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 23425 . T C 88.0 min_af_0.050000 AF=0.000985;DP=17263;DP4=3692,13549,3,15;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P621|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 23439 . C T 100.0 min_af_0.050000 AF=0.001053;DP=17099;DP4=3589,13484,4,14;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A626V|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 23462 . C T 126.0 min_af_0.050000 AF=0.001338;DP=17185;DP4=3035,14116,6,20;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R634C|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 23493 . A G 90.0 min_af_0.050000 AF=0.000907;DP=20942;DP4=6938,13963,23,16;SB=29;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q644R|1273|S|protein_coding|CODING|GU280_gp02|1|G) +NC_045512.2 23552 . ATACCCATTGGTGCAGGTATATGCGCTAGT A 145.0 min_af_0.050000 AF=0.001893;DP=5811;DP4=4532,1270,7,4;HRUN=1;SB=5;INDEL;EFF=FRAME_SHIFT(HIGH||cccattggtgcaggtatatgcgctagttat/|PIGAGICASY665|1273|S|protein_coding|CODING|GU280_gp02|1|A|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 23568 . GTA G 66.0 min_af_0.050000 AF=0.001026;DP=5846;DP4=4545,1316,5,1;HRUN=1;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||atatgc/|IC670|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 23616 . G A 89.0 min_af_0.050000 AF=0.003866;DP=2328;DP4=1117,1202,1,8;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R685H|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 24182 . A C 147.0 min_af_0.050000 AF=0.020997;DP=381;DP4=276,97,4,4;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Cct|T874P|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 24728 . G A 82.0 min_af_0.050000 AF=0.000723;DP=27644;DP4=22524,5093,18,2;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1056T|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 24729 . C T 323.0 min_af_0.050000 AF=0.001663;DP=27657;DP4=22503,5095,36,12;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1056V|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 24752 . C T 95.0 min_af_0.050000 AF=0.000795;DP=28914;DP4=22721,6154,23,6;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1064Y|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 24770 . G A 136.0 min_af_0.050000 AF=0.000946;DP=28532;DP4=22916,5573,25,4;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1070T|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 24793 . T C 92.0 min_af_0.050000 AF=0.000755;DP=29133;DP4=22850,6250,21,5;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T1077|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 24794 . G A 113.0 min_af_0.050000 AF=0.000855;DP=29231;DP4=22852,6337,22,6;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A1078T|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 24799 . T C 150.0 min_af_0.050000 AF=0.000995;DP=29150;DP4=22833,6271,29,7;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P1079|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 24800 . G A 114.0 min_af_0.050000 AF=0.000854;DP=29273;DP4=22886,6348,22,4;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A1080T|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 24933 . G T 1263.0 min_af_0.050000 AF=0.004328;DP=27725;DP4=5738,21835,28,110;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G1124V|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 24939 . G A 96.0 min_af_0.050000 AF=0.000787;DP=27943;DP4=5902,22003,3,25;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C1126Y|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 24942 . A T 756.0 min_af_0.050000 AF=0.002979;DP=27862;DP4=5854,21905,11,79;SB=14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D1127V|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 24966 . A T 102.0 min_af_0.050000 AF=0.000825;DP=27895;DP4=6029,21831,14,11;SB=37;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aTc|N1135I|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 24985 . G A 81.0 min_af_0.050000 AF=0.000720;DP=27773;DP4=5873,21863,3,23;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L1141|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 24986 . C T 113.0 min_af_0.050000 AF=0.000866;DP=27711;DP4=5859,21820,2,25;SB=10;EFF=STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q1142*|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 25007 . A G 87.0 min_af_0.050000 AF=0.000720;DP=27762;DP4=6070,21661,5,19;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K1149E|1273|S|protein_coding|CODING|GU280_gp02|1|G) +NC_045512.2 25049 . G T 81.0 min_af_0.050000 AF=0.000780;DP=25627;DP4=4432,21148,5,26;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D1163Y|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 25345 . T C 133.0 min_af_0.050000 AF=0.001541;DP=12330;DP4=9912,2395,16,4;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1261|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 25452 . C T 83.0 min_af_0.050000 AF=0.002103;DP=4754;DP4=2545,2198,5,6;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I20|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) +NC_045512.2 25527 . G A 91.0 min_af_0.050000 AF=0.001163;DP=13756;DP4=2772,10956,6,12;SB=6;EFF=STOP_GAINED(HIGH|NONSENSE|tgG/tgA|W45*|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) +NC_045512.2 25543 . G A 191.0 min_af_0.050000 AF=0.001876;DP=13859;DP4=2806,11016,10,18;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A51T|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) +NC_045512.2 25785 . G T 1368.0 PASS AF=0.078772;DP=749;DP4=366,323,30,29;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgG/tgT|W131C|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) +NC_045512.2 25963 . G A 80.0 min_af_0.050000 AF=0.000889;DP=20248;DP4=15478,4744,17,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E191K|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) +NC_045512.2 26042 . C T 2421.0 min_af_0.050000 AF=0.008776;DP=20282;DP4=15383,4712,142,41;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T217I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) +NC_045512.2 26044 . C G 2272.0 min_af_0.050000 AF=0.008352;DP=20115;DP4=15297,4638,134,37;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q218E|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) +NC_045512.2 26046 . A G 2419.0 min_af_0.050000 AF=0.008854;DP=20216;DP4=15316,4716,140,41;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q218|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) +NC_045512.2 26054 . C T 177.0 min_af_0.050000 AF=0.001501;DP=19993;DP4=15345,4610,21,10;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T221I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) +NC_045512.2 26057 . A C 149.0 min_af_0.050000 AF=0.002423;DP=11556;DP4=6976,4538,18,14;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gCc|D222A|275|ORF3a|protein_coding|CODING|GU280_gp03|1|C) +NC_045512.2 26089 . T A 308.0 min_af_0.050000 AF=0.004038;DP=7430;DP4=3377,4013,7,26;SB=23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Aac|Y233N|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) +NC_045512.2 26103 . T A 739.0 min_af_0.050000;sb_fdr AF=0.007772;DP=7591;DP4=3673,3855,56,5;SB=118;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V237|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) +NC_045512.2 26141 . A T 370.0 min_af_0.050000 AF=0.004848;DP=7425;DP4=4276,3106,13,23;SB=19;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gTc|D250V|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) +NC_045512.2 26194 . A T 163.0 min_af_0.050000 AF=0.001439;DP=20158;DP4=4634,15473,14,19;SB=19;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acg/Tcg|T268S|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) +NC_045512.2 26209 . G A 120.0 min_af_0.050000 AF=0.001098;DP=20035;DP4=4361,15644,4,20;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V273M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) +NC_045512.2 26444 . C T 133.0 min_af_0.050000 AF=0.009395;DP=958;DP4=226,723,2,7;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S67F|75|E|protein_coding|CODING|GU280_gp04|1|T) +NC_045512.2 26542 . C A 294.0 min_af_0.050000 AF=0.005601;DP=4285;DP4=300,3952,0,24;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aAt|T7N|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 26545 . T G 596.0 min_af_0.050000 AF=0.002632;DP=27734;DP4=23608,4048,50,25;SB=43;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aGt|I8S|222|M|protein_coding|CODING|GU280_gp05|1|G) +NC_045512.2 26554 . A G 231.0 min_af_0.050000 AF=0.001343;DP=28305;DP4=23755,4496,36,6;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E11G|222|M|protein_coding|CODING|GU280_gp05|1|G) +NC_045512.2 26566 . A G 106.0 min_af_0.050000 AF=0.001211;DP=28909;DP4=23882,4962,34,6;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K15R|222|M|protein_coding|CODING|GU280_gp05|1|G) +NC_045512.2 26695 . G C 248.0 min_af_0.050000 AF=0.003064;DP=9137;DP4=3972,5129,3,25;SB=34;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W58S|222|M|protein_coding|CODING|GU280_gp05|1|C) +NC_045512.2 26769 . G A 113.0 min_af_0.050000 AF=0.000875;DP=28587;DP4=5339,23210,6,24;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A83T|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 26774 . GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTT G 115.0 min_af_0.050000 AF=0.000525;DP=28594;DP4=5378,23236,0,15;HRUN=2;SB=10;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgtttgcg/gcg|ACLVGLMWLSYFIASFRLFA85A|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME) +NC_045512.2 26774 . GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT G 83.0 min_af_0.050000 AF=0.000420;DP=28594;DP4=5378,23236,0,12;HRUN=2;SB=8;INDEL;EFF=FRAME_SHIFT(HIGH||gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/|ACLVGLMWLSYFIASFRLF85|222|M|protein_coding|CODING|GU280_gp05|1|G);LOF=(M|GU280_gp05|1|1.00) +NC_045512.2 26775 . GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT G 351.0 min_af_0.050000 AF=0.001157;DP=28524;DP4=5373,23234,4,29;HRUN=1;SB=2;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc|CLVGLMWLSYFIASF86F|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME) +NC_045512.2 26779 . GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT G 869.0 min_af_0.050000 AF=0.002271;DP=28626;DP4=5385,23256,8,57;HRUN=1;SB=6;INDEL;EFF=FRAME_SHIFT(HIGH||gtaggcttgatgtggctcagctacttcattgcttctttc/|VGLMWLSYFIASF88|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00) +NC_045512.2 26786 . AGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT A 940.0 min_af_0.050000 AF=0.002413;DP=28595;DP4=5340,23218,9,60;HRUN=2;SB=5;INDEL;EFF=FRAME_SHIFT(HIGH||ggcttgatgtggctcagctacttcattgcttctttc/|GLMWLSYFIASF89|222|M|protein_coding|CODING|GU280_gp05|1|A);LOF=(M|GU280_gp05|1|1.00) +NC_045512.2 26798 . G A 105.0 min_af_0.050000 AF=0.000868;DP=28812;DP4=5462,23064,5,20;SB=0;EFF=STOP_GAINED(HIGH|NONSENSE|tgG/tgA|W92*|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 26839 . C T 208.0 min_af_0.050000 AF=0.001347;DP=28947;DP4=4990,23908,12,31;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T106M|222|M|protein_coding|CODING|GU280_gp05|1|T) +NC_045512.2 26885 . C T 108.0 min_af_0.050000 AF=0.000780;DP=42334;DP4=17203,25082,14,21;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N121|222|M|protein_coding|CODING|GU280_gp05|1|T) +NC_045512.2 26888 . G A 81.0 min_af_0.050000 AF=0.000638;DP=42299;DP4=17150,25099,12,22;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V122|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 26889 . C T 167.0 min_af_0.050000 AF=0.000971;DP=42214;DP4=17062,25099,15,30;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P123S|222|M|protein_coding|CODING|GU280_gp05|1|T) +NC_045512.2 27097 . GT G 88.0 min_af_0.050000 AF=0.000583;DP=20569;DP4=4890,15748,3,9;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F193|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00) +NC_045512.2 27131 . CTATAAAT C 110.0 min_af_0.050000 AF=0.000623;DP=20859;DP4=5002,15909,3,10;HRUN=1;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||tataaatta/|YKL204|222|M|protein_coding|CODING|GU280_gp05|1|C|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00) +NC_045512.2 27133 . ATAAATT A 226.0 min_af_0.050000 AF=0.001049;DP=20965;DP4=5016,15929,9,13;HRUN=1;SB=11;INDEL;EFF=STOP_GAINED+CODON_CHANGE_PLUS_CODON_DELETION(HIGH||tataaatta/taa|YKL204*|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 27190 . AAGTGACAACAGATGTTTCATCTCGTTGACTT A 97.0 min_af_0.050000 AF=0.000617;DP=24308;DP4=20706,18252,14,1;HRUN=2;SB=28;INDEL;EFF=GENE_FUSION(HIGH|||||M+ORF6||CODING|||A),FRAME_SHIFT+STOP_LOST+SPLICE_SITE_REGION(HIGH||taa/|*223|222|M|protein_coding|CODING|GU280_gp05|1|A),FRAME_SHIFT+START_LOST(HIGH||atgtttcatctcgttgacttt/|MFHLVDF1|61|ORF6|protein_coding|CODING|GU280_gp06|1|A);LOF=(ORF6|GU280_gp06|1|1.00) +NC_045512.2 27214 . G A 104.0 min_af_0.050000 AF=0.001051;DP=22836;DP4=18857,3927,21,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V5I|61|ORF6|protein_coding|CODING|GU280_gp06|1|A) +NC_045512.2 27285 . T A 292.0 min_af_0.050000 AF=0.001761;DP=22714;DP4=18427,4236,40,2;SB=17;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N28K|61|ORF6|protein_coding|CODING|GU280_gp06|1|A) +NC_045512.2 27335 . C T 588.0 min_af_0.050000 AF=0.006257;DP=7831;DP4=4278,3502,31,18;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T45I|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) +NC_045512.2 27344 . A T 1040.0 min_af_0.050000 AF=0.009986;DP=7811;DP4=4348,3381,53,26;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aTa|K48I|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) +NC_045512.2 27345 . A T 1026.0 min_af_0.050000 AF=0.009985;DP=7812;DP4=4358,3374,52,26;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K48N|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) +NC_045512.2 27354 . A G 1255.0 min_af_0.050000 AF=0.011517;DP=7641;DP4=4387,3162,62,27;SB=15;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q51|61|ORF6|protein_coding|CODING|GU280_gp06|1|G) +NC_045512.2 27720 . TATA T 301.0 PASS AF=0.056701;DP=194;DP4=56,129,6,5;HRUN=1;SB=9;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ataaca/aca|IT110T|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T|INFO_REALIGN_3_PRIME) +NC_045512.2 28019 . T C 80.0 min_af_0.050000 AF=0.006079;DP=987;DP4=283,698,0,6;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y42|121|ORF8|protein_coding|CODING|GU280_gp09|1|C) +NC_045512.2 28148 . T C 122.0 min_af_0.050000 AF=0.001204;DP=19103;DP4=16383,2676,25,3;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P85|121|ORF8|protein_coding|CODING|GU280_gp09|1|C) +NC_045512.2 28195 . G A 84.0 min_af_0.050000 AF=0.000961;DP=19771;DP4=16165,3583,15,4;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R101H|121|ORF8|protein_coding|CODING|GU280_gp09|1|A) +NC_045512.2 28232 . C T 88.0 min_af_0.050000 AF=0.000926;DP=19437;DP4=16091,3321,16,2;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D113|121|ORF8|protein_coding|CODING|GU280_gp09|1|T) +NC_045512.2 28326 . G T 189.0 min_af_0.050000 AF=0.001431;DP=20959;DP4=4181,16743,5,28;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G18V|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 28380 . G A 100.0 min_af_0.050000 AF=0.000983;DP=20349;DP4=3516,16795,6,21;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R36Q|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 28406 . TTACCCAATA T 99.0 min_af_0.050000 AF=0.000588;DP=20419;DP4=3137,17295,0,12;HRUN=3;SB=6;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttacccaataat/tat|LPNN45Y|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 28436 . G A 96.0 min_af_0.050000 AF=0.000921;DP=22792;DP4=5504,17257,4,21;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A55T|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 28714 . C T 124.0 min_af_0.050000 AF=0.001581;DP=12018;DP4=8559,3430,15,9;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G147|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 28801 . C A 85.0 min_af_0.050000 AF=0.001339;DP=11202;DP4=8430,2743,10,10;SB=18;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agC/agA|S176R|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 28876 . C T 84.0 min_af_0.050000 AF=0.002074;DP=5303;DP4=2390,2902,5,6;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S201|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 28987 . CCAA C 414.0 min_af_0.050000 AF=0.002606;DP=11513;DP4=2411,9107,7,23;HRUN=2;SB=0;INDEL;EFF=CODON_DELETION(MODERATE||caa/|Q242|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME) +NC_045512.2 29027 . G T 203.0 min_af_0.050000 AF=0.001223;DP=29446;DP4=18810,10572,30,14;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A252S|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29029 . T C 1891.0 min_af_0.050000 AF=0.005500;DP=29452;DP4=18773,10482,91,92;SB=41;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A252|419|N|protein_coding|CODING|GU280_gp10|1|C) +NC_045512.2 29039 . A T 6489.0 min_af_0.050000 AF=0.014020;DP=29815;DP4=18712,10662,202,224;SB=108;EFF=STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K256*|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29049 . G A 590.0 min_af_0.050000 AF=0.003061;DP=23194;DP4=18861,4251,67,9;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R259Q|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 29067 . CTAAAGCATACAATG C 141.0 min_af_0.050000 AF=0.000696;DP=22988;DP4=18360,4666,14,2;HRUN=1;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||aaagcatacaatgtaaca/|KAYNVT266|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00) +NC_045512.2 29095 . C T 83.0 min_af_0.050000 AF=0.000864;DP=23152;DP4=18350,4772,17,5;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F274|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29110 . A G 84.0 min_af_0.050000 AF=0.000869;DP=23018;DP4=18316,4667,14,8;SB=9;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P279|419|N|protein_coding|CODING|GU280_gp10|1|G) +NC_045512.2 29114 . C T 94.0 min_af_0.050000 AF=0.000914;DP=22969;DP4=18282,4644,17,7;SB=5;EFF=STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q281*|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29187 . C T 173.0 min_af_0.050000 AF=0.002658;DP=8276;DP4=4583,3668,9,13;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A305V|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29188 . A G 140.0 min_af_0.050000 AF=0.002202;DP=8175;DP4=4555,3592,7,14;SB=13;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A305|419|N|protein_coding|CODING|GU280_gp10|1|G) +NC_045512.2 29195 . GC G 376.0 min_af_0.050000 AF=0.003461;DP=8089;DP4=4612,3478,15,13;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ccc/|P309|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00) +NC_045512.2 29227 . G T 10969.0 min_af_0.050000 AF=0.028346;DP=22155;DP4=4416,17071,181,465;SB=50;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcT|S318|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29229 . G A 85.0 min_af_0.050000 AF=0.000857;DP=23341;DP4=4584,18726,4,21;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R319H|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 29247 . C T 127.0 min_af_0.050000 AF=0.001148;DP=23526;DP4=4650,18843,5,23;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T325I|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29254 . G A 281.0 min_af_0.050000 AF=0.001700;DP=23530;DP4=4654,18818,10,39;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S327|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 29259 . C T 85.0 min_af_0.050000 AF=0.000897;DP=23401;DP4=4563,18811,7,16;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T329M|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29279 . G A 136.0 min_af_0.050000 AF=0.001077;DP=23215;DP4=4317,18858,4,26;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A336T|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 29280 . C T 85.0 min_af_0.050000 AF=0.000821;DP=23150;DP4=4303,18812,2,21;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A336V|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29287 . A T 94.0 min_af_0.050000 AF=0.000906;DP=23185;DP4=4260,18897,3,19;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K338N|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29348 . G A 93.0 min_af_0.050000 AF=0.000890;DP=22464;DP4=3870,18549,4,17;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A359T|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 29377 . TA T 111.0 min_af_0.050000 AF=0.003745;DP=2136;DP4=1755,642,5,3;HRUN=5;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K370|419|N|protein_coding|CODING|GU280_gp10|1|T|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1085080.vcf Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,268 @@ +##fileformat=VCFv4.0 +##fileDate=20201106 +##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-14951 -o /data/dnb03/galaxy_db/job_working_directory/012/246/12246261/tmp/lofreq2_call_parallelpau7d8kw/0.vcf.gz reads.bam +##reference=reference.fa +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> +##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> +##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant)."> +##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> +##FILTER=<ID=min_snvqual_76,Description="Minimum SNV Quality (Phred) 76"> +##FILTER=<ID=min_indelqual_61,Description="Minimum Indel Quality (Phred) 61"> +##FILTER=<ID=min_snvqual_80,Description="Minimum SNV Quality (Phred) 80"> +##FILTER=<ID=min_indelqual_65,Description="Minimum Indel Quality (Phred) 65"> +##FILTER=<ID=min_af_0.050000,Description="Minimum allele frequency 0.050000"> +##FILTER=<ID=min_dp_5,Description="Minimum Coverage 5"> +##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000"> +##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani" +##SnpEffCmd="SnpEff -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -stats /data/dnb03/galaxy_db/job_working_directory/012/246/12246328/outputs/galaxy_dataset_1054f879-0756-4754-86b9-66ab53b4f190.dat NC_045512.2 /data/dnb03/galaxy_db/files/9/8/a/dataset_98aa5c97-caf5-43bb-8d6e-033816a165dc.dat " +##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype [ | ERRORS | WARNINGS ] )' "> +##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +#CHROM POS ID REF ALT QUAL FILTER INFO +NC_045512.2 186 . C T 134.0 min_af_0.050000 AF=0.002111;DP=9950;DP4=7060,2864,14,8;SB=3 +NC_045512.2 241 . C T 49314.0 PASS AF=0.991085;DP=4711;DP4=0,2,2421,2286;SB=6 +NC_045512.2 295 . GA G 86.0 min_af_0.050000 AF=0.000776;DP=12892;DP4=2790,10130,3,7;HRUN=4;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||aca/|T12|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aca/|T12|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aca/|T12|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aca/|T12|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 320 . C T 130.0 min_af_0.050000 AF=0.001651;DP=12717;DP4=2676,10012,6,18;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P19S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P19S|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P19S|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P19S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T) +NC_045512.2 343 . G A 85.0 min_af_0.050000 AF=0.000997;DP=20063;DP4=9201,10833,11,13;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V26|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V26|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V26|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V26|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A) +NC_045512.2 346 . C T 87.0 min_af_0.050000 AF=0.000947;DP=20061;DP4=9173,10861,6,14;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L27|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L27|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L27|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L27|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T) +NC_045512.2 384 . C T 113.0 min_af_0.050000 AF=0.001059;DP=19826;DP4=8681,11111,8,18;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S40L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S40L|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S40L|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S40L|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T) +NC_045512.2 408 . A G 92.0 min_af_0.050000 AF=0.001520;DP=9869;DP4=7607,2236,8,7;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D48G|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D48G|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D48G|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D48G|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G) +NC_045512.2 439 . A G 136.0 min_af_0.050000 AF=0.003018;DP=9942;DP4=7528,2377,22,11;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K58|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K58|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K58|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K58|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G) +NC_045512.2 443 . GT G 152.0 min_af_0.050000 AF=0.001419;DP=9867;DP4=7517,2353,10,4;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttg/|L61|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 645 . G A 139.0 min_af_0.050000 AF=0.001901;DP=9469;DP4=1920,7528,7,13;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G127D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G127D|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G127D|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G127D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A) +NC_045512.2 685 . AAAGTCATTT A 483.0 min_af_0.050000 AF=0.003415;DP=9662;DP4=2267,7379,9,24;HRUN=3;SB=1;INDEL;EFF=CODON_DELETION(MODERATE||aagtcattt/|KSF141|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_DELETION(MODERATE||aagtcattt/|KSF141|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_DELETION(MODERATE||aagtcattt/|KSF141|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_DELETION(MODERATE||aagtcattt/|KSF141|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A) +NC_045512.2 1019 . C T 99.0 min_af_0.050000 AF=0.001342;DP=11174;DP4=9196,1955,12,3;SB=1;EFF=STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q252*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q252*|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q72*|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q72*|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04) +NC_045512.2 1075 . T C 87.0 min_af_0.050000 AF=0.001237;DP=11322;DP4=9045,2250,18,3;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C270|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C270|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C90|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C90|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1115 . A T 412.0 min_af_0.050000 AF=0.008698;DP=3449;DP4=1366,2051,2,29;SB=42;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I284F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I284F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I104F|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I104F|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1133 . A T 223.0 min_af_0.050000 AF=0.005443;DP=3491;DP4=1491,1981,17,2;SB=42;EFF=STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K290*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K290*|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K110*|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K110*|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04) +NC_045512.2 1224 . T C 100.0 min_af_0.050000 AF=0.001457;DP=10296;DP4=1820,8452,7,12;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L320P|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L320P|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L140P|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L140P|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1304 . G T 221.0 min_af_0.050000 AF=0.002447;DP=10217;DP4=1929,8259,6,19;SB=3;EFF=STOP_GAINED(HIGH|NONSENSE|Gag/Tag|E347*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),STOP_GAINED(HIGH|NONSENSE|Gag/Tag|E347*|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),STOP_GAINED(HIGH|NONSENSE|Gag/Tag|E167*|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),STOP_GAINED(HIGH|NONSENSE|Gag/Tag|E167*|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04) +NC_045512.2 1644 . A C 80.0 min_af_0.050000 AF=0.001682;DP=7133;DP4=5888,1231,7,5;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N460T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N460T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N280T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N280T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1647 . T A 91.0 min_af_0.050000 AF=0.001680;DP=7142;DP4=5854,1271,8,5;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I461N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I461N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I281N|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I281N|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1656 . T A 90.0 min_af_0.050000 AF=0.001807;DP=7195;DP4=5827,1352,9,5;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V464D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V464D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V284D|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V284D|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1695 . T G 82.0 min_af_0.050000 AF=0.002029;DP=7394;DP4=5871,1505,11,5;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tGg|L477W|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tGg|L477W|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tGg|L297W|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tGg|L297W|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1702 . T C 195.0 min_af_0.050000 AF=0.003394;DP=7366;DP4=5832,1483,22,5;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S479|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S479|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S299|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S299|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1914 . G A 150.0 min_af_0.050000 AF=0.002571;DP=6613;DP4=1088,5503,6,12;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R550H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R550H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R370H|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R370H|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 3037 . C T 19713.0 PASS AF=0.986891;DP=534;DP4=0,0,268,264;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 3290 . C G 128.0 min_af_0.050000 AF=0.002266;DP=6620;DP4=5436,1163,11,4;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q1009E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q1009E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q191E|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q191E|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4174 . TA T 142.0 min_af_0.050000 AF=0.001279;DP=11728;DP4=9312,2441,11,4;HRUN=5;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K1305|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K1305|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K487|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K487|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 4185 . G T 162.0 min_af_0.050000 AF=0.002100;DP=11907;DP4=9344,2535,12,13;SB=31;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G1307V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G1307V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G489V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G489V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4189 . C T 93.0 min_af_0.050000 AF=0.001263;DP=11879;DP4=9326,2523,16,3;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G1308|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G1308|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G490|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G490|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4195 . T C 80.0 min_af_0.050000 AF=0.001184;DP=11824;DP4=9348,2459,12,3;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T1310|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T1310|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T492|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T492|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4308 . A G 82.0 min_af_0.050000 AF=0.001455;DP=12371;DP4=2527,9825,6,12;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K1348R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K1348R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K530R|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K530R|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4371 . G T 90.0 min_af_0.050000 AF=0.001210;DP=13227;DP4=3595,9586,3,17;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G1369V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G1369V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G551V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G551V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5601 . T C 105.0 min_af_0.050000 AF=0.001463;DP=10254;DP4=6843,3393,12,4;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tCt|F1779S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tCt|F1779S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tCt|F961S|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tCt|F961S|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5743 . G C 1464.0 min_af_0.050000;sb_fdr AF=0.026248;DP=3124;DP4=1517,1525,11,71;SB=109;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1826D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1826D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1008D|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1008D|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5744 . T C 1686.0 min_af_0.050000 AF=0.029789;DP=3122;DP4=1522,1505,19,75;SB=82;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1827H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1827H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1009H|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1009H|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5765 . G A 199.0 min_af_0.050000 AF=0.005792;DP=3108;DP4=1726,1363,6,12;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1834S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1834S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1016S|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1016S|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5766 . G C 86.0 min_af_0.050000 AF=0.003186;DP=3139;DP4=1768,1358,2,8;SB=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G1834A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G1834A|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G1016A|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G1016A|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5812 . C T 405.0 min_af_0.050000 AF=0.004460;DP=8745;DP4=1886,6812,12,30;SB=5;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1849|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1849|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1031|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1031|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5818 . TTTAC T 239.0 min_af_0.050000 AF=0.002052;DP=8773;DP4=1938,6866,3,15;HRUN=3;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||cttaca/|LT1853|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||cttaca/|LT1853|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||cttaca/|LT1035|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||cttaca/|LT1035|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 6199 . T C 116.0 min_af_0.050000 AF=0.001229;DP=26862;DP4=19785,7035,23,11;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1978|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1978|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1160|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1160|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6242 . C T 100.0 min_af_0.050000 AF=0.000795;DP=28921;DP4=20236,8653,20,6;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1993Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1993Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1175Y|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1175Y|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6255 . C T 329.0 min_af_0.050000 AF=0.001751;DP=25699;DP4=20282,5363,36,11;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1997V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1997V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1179V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1179V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6297 . G A 84.0 min_af_0.050000 AF=0.000761;DP=26296;DP4=19945,6320,17,6;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R2011H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R2011H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R1193H|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R1193H|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6312 . CA C 376.0 min_af_0.050000 AF=0.001389;DP=25918;DP4=19826,6183,28,8;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K2017|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K2017|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1199|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1199|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 6352 . G C 100.0 min_af_0.050000 AF=0.001539;DP=9749;DP4=4152,5577,7,8;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaC|K2029N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaC|K2029N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaC|K1211N|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaC|K1211N|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6409 . T C 110.0 min_af_0.050000 AF=0.000930;DP=23646;DP4=4691,18919,4,20;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S2048|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S2048|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1230|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1230|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6416 . G A 95.0 min_af_0.050000 AF=0.000855;DP=23400;DP4=4566,18808,3,19;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V2051I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V2051I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V1233I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V1233I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6503 . G A 133.0 min_af_0.050000 AF=0.001139;DP=20199;DP4=3118,17049,10,19;SB=20;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A2080T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A2080T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1262T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1262T|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 7021 . TTTA T 73.0 min_af_0.050000 AF=0.002296;DP=2178;DP4=398,1780,0,5;HRUN=4;SB=2;INDEL;EFF=CODON_DELETION(MODERATE||tta/|L2253|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),CODON_DELETION(MODERATE||tta/|L2253|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),CODON_DELETION(MODERATE||tta/|L1435|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),CODON_DELETION(MODERATE||tta/|L1435|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 7889 . GT G 353.0 min_af_0.050000 AF=0.005331;DP=4314;DP4=884,3413,6,17;HRUN=5;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F2543|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F2543|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F1725|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F1725|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 7986 . A G 84.0 min_af_0.050000 AF=0.001676;DP=6563;DP4=2932,3615,5,8;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q2574R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q2574R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q1756R|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q1756R|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 8883 . T C 80.0 min_af_0.050000 AF=0.010616;DP=471;DP4=88,377,2,3;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I2873T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I2873T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I110T|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I110T|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 8916 . T C 128.0 min_af_0.050000 AF=0.003252;DP=3997;DP4=3121,863,11,2;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTc/tCc|F2884S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTc/tCc|F2884S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTc/tCc|F121S|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTc/tCc|F121S|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 8927 . GT G 108.0 min_af_0.050000 AF=0.002195;DP=4100;DP4=3161,931,6,3;HRUN=5;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F2889|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F2889|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F126|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F126|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 9014 . G A 85.0 min_af_0.050000 AF=0.002464;DP=4058;DP4=3162,885,7,3;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A2917T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A2917T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A154T|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A154T|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 9016 . T C 93.0 min_af_0.050000 AF=0.002467;DP=4054;DP4=3162,882,8,2;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A2917|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A2917|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A154|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A154|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 9208 . T C 84.0 min_af_0.050000 AF=0.002427;DP=3708;DP4=685,3012,3,7;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S2981|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S2981|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S218|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S218|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 9600 . T C 90.0 min_af_0.050000 AF=0.001700;DP=8237;DP4=6499,1722,10,4;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L3112S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L3112S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L349S|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L349S|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 10046 . GTTT G 72.0 min_af_0.050000 AF=0.006144;DP=651;DP4=152,496,1,3;HRUN=4;SB=0;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttttg/gtg|VL3261V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttttg/gtg|VL3261V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttttg/gtg|VL498V|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttttg/gtg|VL498V|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME) +NC_045512.2 10386 . CT C 99.0 min_af_0.050000 AF=0.002298;DP=3481;DP4=2009,1466,4,4;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||tca/|S3376|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tca/|S3376|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tca/|S113|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tca/|S113|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 11036 . CTTTTAG C 127.0 min_af_0.050000 AF=0.001090;DP=11931;DP4=10092,1826,12,1;HRUN=4;SB=1;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttttagtc/gtc|VLV3593V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttttagtc/gtc|VLV3593V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttttagtc/gtc|VLV24V|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttttagtc/gtc|VLV24V|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME) +NC_045512.2 11067 . C T 159.0 min_af_0.050000 AF=0.001731;DP=12712;DP4=10344,2335,18,10;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S3601F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S3601F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S32F|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S32F|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11071 . G GTTC 49314.0 PASS AF=0.919205;DP=12736;DP4=800,227,9565,2142;HRUN=2;SB=24;INDEL;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTTt|F3604FF|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|GTTC|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTTt|F3604FF|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|GTTC|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTTt|F35FF|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|GTTC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTTt|F35FF|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|GTTC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME) +NC_045512.2 11074 . C CTTCT 3762.0 min_af_0.050000 AF=0.026300;DP=13004;DP4=10107,2533,282,60;HRUN=8;SB=5;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/ttCTTTt|F3604FF?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|CTTCT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTTTt|F3604FF?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|CTTCT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTTTt|F35FF?|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|CTTCT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTTTt|F35FF?|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|CTTCT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 11075 . T TTC 7808.0 min_af_0.050000 AF=0.025871;DP=13026;DP4=10138,2548,273,64;HRUN=8;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/ttCTt|F3604F?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|TTC|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTt|F3604F?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|TTC|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTt|F35F?|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|TTC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTt|F35F?|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|TTC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 11075 . T TTCC 208.0 min_af_0.050000 AF=0.001382;DP=13026;DP4=10138,2548,15,3;HRUN=8;SB=0;INDEL;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCCTt|F3604FL|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|TTCC|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCCTt|F3604FL|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|TTCC|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCCTt|F35FL|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|TTCC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCCTt|F35FL|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|TTCC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME) +NC_045512.2 11076 . T TCTC 120.0 min_af_0.050000 AF=0.000915;DP=13115;DP4=10415,2686,8,4;HRUN=8;SB=5;INDEL;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTCt|F3604FS|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|TCTC),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTCt|F3604FS|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|TCTC),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTCt|F35FS|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|TCTC|WARNING_TRANSCRIPT_NO_START_CODON),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTCt|F35FS|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|TCTC|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11077 . T C 217.0 min_af_0.050000 AF=0.008991;DP=13124;DP4=10364,2639,66,55;SB=90;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F3604|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F3604|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F35|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F35|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11083 . G T 86.0 min_af_0.050000 AF=0.003262;DP=13183;DP4=10380,2749,31,18;SB=19;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L3606F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L3606F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L37F|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L37F|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11104 . T C 126.0 min_af_0.050000 AF=0.001408;DP=13493;DP4=10490,2969,16,6;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P3613|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P3613|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P44|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P44|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11139 . C T 123.0 min_af_0.050000 AF=0.001387;DP=13695;DP4=10485,3180,15,11;SB=14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A3625V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A3625V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A56V|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A56V|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11442 . C T 1697.0 min_af_0.050000 AF=0.020029;DP=4893;DP4=3611,1179,71,28;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3726V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3726V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A157V|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A157V|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11653 . CT C 106.0 min_af_0.050000 AF=0.001023;DP=10755;DP4=6029,4718,5,6;HRUN=4;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||tgt/|C3798|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C3798|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C229|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C229|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 11851 . G A 153.0 min_af_0.050000 AF=0.002485;DP=6840;DP4=1562,5257,2,16;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M3862I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M3862I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M3I|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M3I|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11866 . C T 107.0 min_af_0.050000 AF=0.001932;DP=7247;DP4=1487,5740,4,12;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C3867|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C3867|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C8|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C8|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12129 . C T 81.0 min_af_0.050000 AF=0.001191;DP=10917;DP4=2183,8720,2,11;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A3955V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A3955V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A13V|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A13V|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12132 . CTT C 80.0 min_af_0.050000 AF=0.000827;DP=10886;DP4=2133,8761,1,8;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F3957|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F3957|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F15|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F15|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 12143 . G A 100.0 min_af_0.050000 AF=0.001349;DP=11858;DP4=3081,8755,3,15;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3960T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3960T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A18T|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A18T|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12662 . G A 100.0 min_af_0.050000 AF=0.001730;DP=8093;DP4=1723,6352,3,11;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4133T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4133T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A191T|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A191T|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12684 . A G 217.0 min_af_0.050000 AF=0.002858;DP=8048;DP4=1686,6335,8,18;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q4140R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q4140R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|cAg/cGg|Q198R|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|cAg/cGg|Q198R|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12769 . G A 80.0 min_af_0.050000 AF=0.001019;DP=18646;DP4=10427,8187,11,9;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A4168|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A4168|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A28|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A28|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13034 . G A 131.0 min_af_0.050000 AF=0.000871;DP=32142;DP4=19137,12963,17,16;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4257T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4257T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13035 . C T 140.0 min_af_0.050000 AF=0.000899;DP=32264;DP4=19148,13078,18,13;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A4257V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A4257V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A4V|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A4V|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13038 . C T 94.0 min_af_0.050000 AF=0.000712;DP=32326;DP4=19147,13141,13,12;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T4258I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T4258I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T5I|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T5I|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13048 . T C 93.0 min_af_0.050000 AF=0.000709;DP=32455;DP4=19069,13247,19,99;SB=209;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4261|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4261|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P8|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P8|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13049 . G A 90.0 min_af_0.050000 AF=0.000707;DP=32554;DP4=19096,13425,19,7;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4262T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4262T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A9T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A9T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13051 . C T 49314.0 PASS AF=0.968256;DP=32510;DP4=506,283,18579,13137;SB=27;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A4262|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A4262|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A9|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A9|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13078 . T C 104.0 min_af_0.050000 AF=0.000897;DP=23404;DP4=18810,4560,17,5;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4271|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4271|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A18|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A18|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13094 . G A 105.0 min_af_0.050000 AF=0.001062;DP=23533;DP4=18300,5201,17,9;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A4277T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A4277T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A24T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A24T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13123 . TG T 121.0 min_af_0.050000 AF=0.000734;DP=23172;DP4=17672,5522,15,2;HRUN=5;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||gga/|G4288|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G4288|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G35|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G35|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) +NC_045512.2 13129 . A G 245.0 min_af_0.050000 AF=0.001754;DP=23381;DP4=17726,5589,47,13;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13142 . AATT A 92.0 min_af_0.050000 AF=0.000522;DP=22996;DP4=17663,5362,11,1;HRUN=2;SB=4;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgt/agt|NC4293S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgt/agt|NC4293S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgt/agt|NC40S|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgt/agt|NC40S|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13182 . A G 82.0 min_af_0.050000 AF=0.001402;DP=9270;DP4=4206,5046,7,9;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q4306R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q4306R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q53R|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q53R|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13235 . G A 121.0 min_af_0.050000 AF=0.001286;DP=21767;DP4=5218,16517,5,24;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4324T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4324T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A71T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A71T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13240 . G A 81.0 min_af_0.050000 AF=0.000912;DP=21941;DP4=5298,16616,7,15;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S4325|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S4325|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S72|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S72|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13267 . A G 88.0 min_af_0.050000 AF=0.000835;DP=22744;DP4=5283,17428,7,13;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I4334M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I4334M|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I81M|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I81M|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13288 . AT A 105.0 min_af_0.050000 AF=0.000617;DP=22682;DP4=5257,17413,2,12;HRUN=4;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||tgt/|C4343|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C4343|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C90|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C90|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) +NC_045512.2 13299 . TA T 84.0 min_af_0.050000 AF=0.000537;DP=22351;DP4=5178,17249,3,9;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K4346|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K4346|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K93|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K93|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) +NC_045512.2 13345 . T C 90.0 min_af_0.050000 AF=0.000911;DP=25238;DP4=8015,17183,13,14;SB=10;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4360|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4360|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P107|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P107|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13385 . G A 118.0 min_af_0.050000 AF=0.002796;DP=6437;DP4=5404,1009,16,3;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G4374S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G4374S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G121S|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G121S|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13451 . G A 128.0 min_af_0.050000 AF=0.002564;DP=5850;DP4=4711,1123,9,6;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4396T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4396T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|12|ORF1ab|protein_coding|CODING|YP_009725312.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13571 . G T 198.0 min_af_0.050000 AF=0.003149;DP=6351;DP4=1257,5071,5,15;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G4436V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G44V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13586 . TA T 78.0 min_af_0.050000 AF=0.001270;DP=6299;DP4=1240,5075,2,6;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||act/|T4443|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||act/|T51|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 13726 . GTT G 148.0 min_af_0.050000 AF=0.000684;DP=24841;DP4=19872,5001,14,3;HRUN=2;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||gtt/|V4488|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),FRAME_SHIFT(HIGH||gtt/|V96|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 13860 . C T 87.0 min_af_0.050000 AF=0.000792;DP=25262;DP4=5217,20021,3,19;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D4532|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D140|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13924 . TG T 102.0 min_af_0.050000 AF=0.000538;DP=24171;DP4=4056,20138,6,7;HRUN=2;SB=18;INDEL;EFF=FRAME_SHIFT(HIGH||tgg/|W4554|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgg/|W162|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 13966 . G A 112.0 min_af_0.050000 AF=0.001448;DP=13119;DP4=11254,1837,19,4;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4568T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A176T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13982 . G A 568.0 min_af_0.050000 AF=0.004640;DP=11637;DP4=9528,2049,31,23;SB=47;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R4573H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R181H|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14000 . T C 109.0 min_af_0.050000 AF=0.001423;DP=11244;DP4=8939,2280,12,9;SB=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L4579S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L187S|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14029 . C T 86.0 min_af_0.050000 AF=0.001223;DP=11445;DP4=8903,2521,14,3;SB=0;EFF=STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R4589*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R197*|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14197 . G A 132.0 min_af_0.050000 AF=0.001690;DP=10653;DP4=2082,8545,5,15;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4645T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A253T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14199 . A G 92.0 min_af_0.050000 AF=0.001321;DP=10596;DP4=2048,8528,3,14;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A4645|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A253|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14408 . C T 38664.0 PASS AF=0.993204;DP=1030;DP4=0,0,481,548;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4715L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P323L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14615 . G A 104.0 min_af_0.050000 AF=0.001821;DP=8237;DP4=6659,1562,14,1;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R4784H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R392H|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14625 . CT C 77.0 min_af_0.050000 AF=0.000960;DP=8333;DP4=6724,1619,4,4;HRUN=4;SB=12;INDEL;EFF=FRAME_SHIFT(HIGH||tca/|S4789|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tca/|S397|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 14779 . A G 83.0 min_af_0.050000 AF=0.001441;DP=8325;DP4=1551,6758,1,12;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N4839D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N447D|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14848 . CTATTTG C 146.0 min_af_0.050000 AF=0.001520;DP=7894;DP4=1373,6562,1,11;HRUN=1;SB=1;INDEL;EFF=CODON_DELETION(MODERATE||tttgta/|FV4863|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||tttgta/|FV471|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME) +NC_045512.2 14852 . TTG T 101.0 min_af_0.050000 AF=0.001143;DP=7873;DP4=1346,6528,2,7;HRUN=3;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||gta/|V4864|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gta/|V472|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 14877 . C T 99.0 min_af_0.050000 AF=0.001715;DP=7580;DP4=1121,6438,1,18;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y4871|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y479|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15324 . C T 49314.0 PASS AF=0.987428;DP=4852;DP4=1,0,3671,1180;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N5020|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N628|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15557 . C T 97.0 min_af_0.050000 AF=0.001120;DP=15182;DP4=12030,3125,16,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A5098V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A706V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15587 . C T 125.0 min_af_0.050000 AF=0.001359;DP=15452;DP4=11989,3428,16,8;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A5108V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A716V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15599 . T C 133.0 min_af_0.050000 AF=0.001423;DP=15462;DP4=11902,3523,20,10;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V5112A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V720A|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15673 . T G 154.0 min_af_0.050000;sb_fdr AF=0.004353;DP=5743;DP4=2619,3096,22,3;SB=47;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Gtt|F5137V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Gtt|F745V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15682 . T A 2513.0 min_af_0.050000 AF=0.025192;DP=5716;DP4=2676,2893,80,66;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y5140N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y748N|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15685 . T A 2366.0 min_af_0.050000 AF=0.024344;DP=5751;DP4=2707,2901,79,63;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L5141M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L749M|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15761 . G C 128.0 min_af_0.050000 AF=0.001343;DP=14896;DP4=3157,11712,5,15;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G5166A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G774A|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15784 . T TGAC 101.0 min_af_0.050000 AF=0.000738;DP=14904;DP4=3226,11771,4,7;HRUN=3;SB=5;INDEL;EFF=STOP_GAINED+CODON_CHANGE_PLUS_CODON_INSERTION(HIGH||ttt/tGACtt|F5174*L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|TGAC),STOP_GAINED+CODON_CHANGE_PLUS_CODON_INSERTION(HIGH||ttt/tGACtt|F782*L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|TGAC|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15788 . AGTC A 102.0 min_af_0.050000 AF=0.000744;DP=14787;DP4=3096,11695,4,7;HRUN=1;SB=5;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aagtca/aaa|KS5175K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aagtca/aaa|KS783K|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15814 . GT G 83.0 min_af_0.050000 AF=0.000757;DP=14525;DP4=2939,11605,0,11;HRUN=5;SB=8;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F5185|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F793|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 15848 . CTG C 87.0 min_af_0.050000 AF=0.000656;DP=15239;DP4=2208,13051,3,7;HRUN=1;SB=7;INDEL;EFF=FRAME_SHIFT(HIGH||actgac/|TD5195|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),FRAME_SHIFT(HIGH||actgac/|TD803|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 15870 . T C 85.0 min_af_0.050000 AF=0.001034;DP=14505;DP4=12263,2225,11,4;SB=5;EFF=SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H5202|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H810|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15878 . G A 117.0 min_af_0.050000 AF=0.001285;DP=14781;DP4=12233,2469,71,2;SB=34;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C5205Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C813Y|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15905 . A G 94.0 min_af_0.050000 AF=0.001148;DP=13939;DP4=10972,2946,14,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q5214R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q822R|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15961 . G A 87.0 min_af_0.050000 AF=0.001195;DP=14228;DP4=11028,3178,13,5;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G5233S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G841S|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 16072 . G T 109.0 min_af_0.050000 AF=0.001374;DP=13827;DP4=2871,10926,3,20;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A5270S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A878S|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 16110 . G A 114.0 min_af_0.050000 AF=0.001321;DP=13630;DP4=2821,10780,7,13;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K5282|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K890|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 16127 . C T 89.0 min_af_0.050000 AF=0.001127;DP=13309;DP4=2569,10720,3,13;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T5288I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T896I|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 16837 . GA G 159.0 min_af_0.050000 AF=0.002455;DP=5295;DP4=4078,1223,11,2;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K5526|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K202|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 17104 . C T 125.0 min_af_0.050000 AF=0.001531;DP=11760;DP4=6999,4735,10,11;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H5614Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H290Y|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 17183 . C T 80.0 min_af_0.050000 AF=0.001379;DP=8701;DP4=6683,2003,8,4;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A5640V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A316V|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 17339 . C T 84.0 min_af_0.050000 AF=0.001407;DP=9239;DP4=2216,7005,2,11;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A5692V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A368V|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 18669 . T C 84.0 min_af_0.050000 AF=0.001497;DP=8014;DP4=6457,1536,13,0;SB=8;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C6135|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C210|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 18687 . CT C 119.0 min_af_0.050000 AF=0.001340;DP=8210;DP4=6530,1683,10,1;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||tcc/|S6143|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tcc/|S218|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 18715 . T C 91.0 min_af_0.050000 AF=0.001573;DP=8263;DP4=6484,1760,12,3;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C6151R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C226R|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 18718 . T C 93.0 min_af_0.050000 AF=0.001566;DP=8302;DP4=6496,1793,10,3;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W6152R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W227R|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 18932 . T C 80.0 min_af_0.050000 AF=0.000882;DP=18140;DP4=10385,7693,13,45;SB=71;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I6223T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I298T|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 18998 . C T 102.0 min_af_0.050000 AF=0.001323;DP=12090;DP4=9600,2461,16,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A6245V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A320V|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19029 . C T 81.0 min_af_0.050000 AF=0.001222;DP=12278;DP4=9707,2551,16,1;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H6255|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H330|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19199 . G A 82.0 min_af_0.050000 AF=0.001118;DP=12520;DP4=2574,9929,3,13;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C6312Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C387Y|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19219 . G A 85.0 min_af_0.050000 AF=0.001153;DP=12139;DP4=2262,9858,5,13;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A6319T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A394T|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19611 . A G 103.0 min_af_0.050000 AF=0.001440;DP=11113;DP4=8992,2101,12,5;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T6449|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T524|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19679 . G T 113.0 min_af_0.050000 AF=0.001523;DP=11821;DP4=9213,2586,16,2;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G6472V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G20V|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19801 . C T 88.0 min_af_0.050000 AF=0.001376;DP=10904;DP4=2116,8770,3,13;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R6513C|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R61C|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19814 . CAG C 239.0 min_af_0.050000 AF=0.001755;DP=10824;DP4=2128,8719,4,15;HRUN=1;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ccagta/|PV6517|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),FRAME_SHIFT(HIGH||ccagta/|PV65|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 19870 . G A 153.0 min_af_0.050000 AF=0.001802;DP=11100;DP4=2451,8624,3,19;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V6536M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V84M|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19970 . C T 98.0 min_af_0.050000 AF=0.007973;DP=878;DP4=657,214,4,3;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A6569V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A117V|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 20937 . G A 108.0 min_af_0.050000 AF=0.001625;DP=10463;DP4=8160,2282,17,3;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T6891|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T93|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 21054 . C T 124.0 min_af_0.050000 AF=0.001835;DP=9808;DP4=1973,7804,4,16;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y6930|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y132|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 21073 . GT G 66.0 min_af_0.050000 AF=0.000733;DP=9549;DP4=1843,7727,2,5;HRUN=2;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||gtt/|V6937|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gtt/|V139|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.04) +NC_045512.2 22218 . GT G 147.0 min_af_0.050000 AF=0.004186;DP=2389;DP4=435,1949,2,8;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||tcg/|S221|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 22643 . T A 801.0 min_af_0.050000 AF=0.005735;DP=11508;DP4=9198,2236,51,17;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C361S|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 22644 . G C 746.0 min_af_0.050000 AF=0.005540;DP=11553;DP4=9197,2280,47,17;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C361S|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 22645 . T A 749.0 min_af_0.050000 AF=0.005544;DP=11543;DP4=9171,2285,52,16;SB=3;EFF=STOP_GAINED(HIGH|NONSENSE|tgT/tgA|C361*|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 22859 . G C 117.0 min_af_0.050000 AF=0.001528;DP=11125;DP4=2468,8618,7,12;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ctt|V433L|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 23132 . GT G 179.0 min_af_0.050000 AF=0.003890;DP=2828;DP4=462,2364,0,11;HRUN=3;SB=6;INDEL;EFF=FRAME_SHIFT(HIGH||tgt/|C525|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 23163 . T C 117.0 min_af_0.050000 AF=0.001396;DP=12895;DP4=9870,2998,17,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V534A|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 23272 . T C 154.0 min_af_0.050000 AF=0.001679;DP=13105;DP4=9931,3147,18,6;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A570|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 23403 . A G 49314.0 PASS AF=0.990102;DP=12730;DP4=3,3,2828,9889;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G) +NC_045512.2 23438 . G A 93.0 min_af_0.050000 AF=0.001224;DP=12256;DP4=2589,9647,4,12;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A626T|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 23439 . C T 145.0 min_af_0.050000 AF=0.001639;DP=12203;DP4=2550,9627,7,15;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A626V|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 23781 . T C 92.0 min_af_0.050000 AF=0.003842;DP=2082;DP4=391,1681,2,7;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M740T|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 24729 . C T 143.0 min_af_0.050000 AF=0.001381;DP=15926;DP4=13029,2871,17,7;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1056V|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 24780 . A G 180.0 min_af_0.050000 AF=0.001600;DP=16878;DP4=13508,3337,21,7;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K1073R|1273|S|protein_coding|CODING|GU280_gp02|1|G) +NC_045512.2 24794 . G A 88.0 min_af_0.050000 AF=0.000996;DP=17063;DP4=13392,3645,14,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A1078T|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 24799 . T C 199.0 min_af_0.050000 AF=0.001639;DP=17083;DP4=13407,3641,25,8;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P1079|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 24942 . A T 607.0 min_af_0.050000 AF=0.003550;DP=16901;DP4=3607,13223,3,62;SB=34;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D1127V|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 24952 . AGGAATT A 84.0 min_af_0.050000 AF=0.000594;DP=16836;DP4=3631,13204,1,9;HRUN=2;SB=1;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggaattgtc/gtc|GIV1131V|1273|S|protein_coding|CODING|GU280_gp02|1|A|INFO_REALIGN_3_PRIME) +NC_045512.2 24972 . T C 153.0 min_af_0.050000 AF=0.001433;DP=16743;DP4=3598,13107,6,22;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V1137A|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 24986 . C T 112.0 min_af_0.050000 AF=0.001156;DP=16431;DP4=3383,13022,5,14;SB=2;EFF=STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q1142*|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 25320 . G A 85.0 min_af_0.050000 AF=0.001360;DP=9562;DP4=7908,1633,14,1;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C1253Y|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 25543 . G A 139.0 min_af_0.050000 AF=0.001802;DP=10546;DP4=2037,8488,5,14;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A51T|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) +NC_045512.2 25587 . CA C 124.0 min_af_0.050000 AF=0.001269;DP=10247;DP4=1857,8407,2,11;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K67|275|ORF3a|protein_coding|CODING|GU280_gp03|1|C|INFO_REALIGN_3_PRIME);LOF=(ORF3a|GU280_gp03|1|1.00) +NC_045512.2 25618 . G A 83.0 min_af_0.050000 AF=0.001432;DP=9779;DP4=1482,8279,5,12;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G76S|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) +NC_045512.2 25936 . C T 174.0 min_af_0.050000 AF=0.002066;DP=10167;DP4=8332,1810,19,3;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H182Y|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) +NC_045512.2 25982 . TA T 80.0 min_af_0.050000 AF=0.000829;DP=10857;DP4=8636,2216,7,2;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K198|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T|INFO_REALIGN_3_PRIME);LOF=(ORF3a|GU280_gp03|1|1.00) +NC_045512.2 26042 . C T 1909.0 min_af_0.050000 AF=0.011118;DP=11693;DP4=8824,2733,98,34;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T217I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) +NC_045512.2 26044 . C G 1780.0 min_af_0.050000 AF=0.010469;DP=11653;DP4=8800,2722,94,32;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q218E|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) +NC_045512.2 26046 . A G 1835.0 min_af_0.050000 AF=0.010734;DP=11738;DP4=8835,2772,96,33;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q218|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) +NC_045512.2 26057 . A C 80.0 min_af_0.050000 AF=0.002228;DP=6734;DP4=3992,2718,9,9;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gCc|D222A|275|ORF3a|protein_coding|CODING|GU280_gp03|1|C) +NC_045512.2 26089 . T A 108.0 min_af_0.050000 AF=0.002580;DP=4652;DP4=2165,2473,2,11;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Aac|Y233N|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) +NC_045512.2 26103 . T A 659.0 min_af_0.050000;sb_fdr AF=0.009765;DP=4813;DP4=2371,2394,43,4;SB=86;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V237|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) +NC_045512.2 26141 . A T 87.0 min_af_0.050000 AF=0.002355;DP=4670;DP4=2711,1943,2,9;SB=19;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gTc|D250V|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) +NC_045512.2 26209 . G A 178.0 min_af_0.050000 AF=0.001966;DP=11696;DP4=2612,9054,8,18;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V273M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) +NC_045512.2 26542 . C A 184.0 min_af_0.050000 AF=0.006467;DP=2165;DP4=107,2043,0,14;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aAt|T7N|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 26545 . T G 296.0 min_af_0.050000 AF=0.002439;DP=15173;DP4=13033,2102,24,13;SB=30;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aGt|I8S|222|M|protein_coding|CODING|GU280_gp05|1|G) +NC_045512.2 26561 . TA T 220.0 min_af_0.050000 AF=0.001461;DP=15742;DP4=13196,2525,18,5;HRUN=5;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K15|222|M|protein_coding|CODING|GU280_gp05|1|T|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00) +NC_045512.2 26774 . GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT G 96.0 min_af_0.050000 AF=0.000650;DP=16926;DP4=3341,13613,1,10;HRUN=2;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/|ACLVGLMWLSYFIASFRLF85|222|M|protein_coding|CODING|GU280_gp05|1|G);LOF=(M|GU280_gp05|1|1.00) +NC_045512.2 26775 . GCTTGT G 95.0 min_af_0.050000 AF=0.000653;DP=16845;DP4=3334,13588,2,9;HRUN=1;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||cttgta/|LV87|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00) +NC_045512.2 26775 . GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT G 134.0 min_af_0.050000 AF=0.000831;DP=16845;DP4=3334,13588,1,13;HRUN=1;SB=4;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc|CLVGLMWLSYFIASF86F|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME) +NC_045512.2 26779 . GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT G 121.0 min_af_0.050000 AF=0.000769;DP=16910;DP4=3320,13623,0,13;HRUN=1;SB=10;INDEL;EFF=FRAME_SHIFT(HIGH||gtaggcttgatgtggctcagctacttcattgcttctttc/|VGLMWLSYFIASF88|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00) +NC_045512.2 26786 . AGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT A 161.0 min_af_0.050000 AF=0.000947;DP=16887;DP4=3297,13606,1,15;HRUN=2;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||ggcttgatgtggctcagctacttcattgcttctttc/|GLMWLSYFIASF89|222|M|protein_coding|CODING|GU280_gp05|1|A);LOF=(M|GU280_gp05|1|1.00) +NC_045512.2 26788 . G A 136.0 min_af_0.050000 AF=0.001295;DP=16992;DP4=3364,13533,3,20;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G89D|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 26814 . G A 83.0 min_af_0.050000 AF=0.000954;DP=16775;DP4=3241,13438,2,16;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A98T|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 26847 . A G 80.0 min_af_0.050000 AF=0.001002;DP=16958;DP4=2751,14184,4,15;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M109V|222|M|protein_coding|CODING|GU280_gp05|1|G) +NC_045512.2 26873 . C T 238.0 min_af_0.050000 AF=0.001445;DP=24907;DP4=10532,14329,20,17;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N117|222|M|protein_coding|CODING|GU280_gp05|1|T) +NC_045512.2 26889 . C T 169.0 min_af_0.050000 AF=0.001294;DP=24736;DP4=10265,14432,18,17;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P123S|222|M|protein_coding|CODING|GU280_gp05|1|T) +NC_045512.2 27093 . T C 87.0 min_af_0.050000 AF=0.001158;DP=12956;DP4=3003,9931,3,12;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S191P|222|M|protein_coding|CODING|GU280_gp05|1|C) +NC_045512.2 27103 . C T 84.0 min_af_0.050000 AF=0.001153;DP=13015;DP4=3020,9979,4,11;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A194V|222|M|protein_coding|CODING|GU280_gp05|1|T) +NC_045512.2 27105 . G A 184.0 min_af_0.050000 AF=0.001854;DP=12942;DP4=3010,9897,7,19;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A195T|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 27133 . ATAAATT A 82.0 min_af_0.050000 AF=0.000704;DP=12790;DP4=2878,9896,2,7;HRUN=1;SB=0;INDEL;EFF=STOP_GAINED+CODON_CHANGE_PLUS_CODON_DELETION(HIGH||tataaatta/taa|YKL204*|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 27133 . ATAAAT A 122.0 min_af_0.050000 AF=0.000938;DP=12790;DP4=2878,9896,2,10;HRUN=1;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttaaac/|LN206|222|M|protein_coding|CODING|GU280_gp05|1|A|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00) +NC_045512.2 27190 . AAGTGACAACAGATGTTTCATCTCGTTGACTT A 84.0 min_af_0.050000 AF=0.000862;DP=12759;DP4=10963,11010,10,1;HRUN=2;SB=22;INDEL;EFF=GENE_FUSION(HIGH|||||M+ORF6||CODING|||A),FRAME_SHIFT+STOP_LOST+SPLICE_SITE_REGION(HIGH||taa/|*223|222|M|protein_coding|CODING|GU280_gp05|1|A),FRAME_SHIFT+START_LOST(HIGH||atgtttcatctcgttgacttt/|MFHLVDF1|61|ORF6|protein_coding|CODING|GU280_gp06|1|A);LOF=(ORF6|GU280_gp06|1|1.00) +NC_045512.2 27282 . G A 92.0 min_af_0.050000 AF=0.001215;DP=12350;DP4=9873,2456,13,6;SB=6;EFF=STOP_GAINED(HIGH|NONSENSE|tgG/tgA|W27*|61|ORF6|protein_coding|CODING|GU280_gp06|1|A) +NC_045512.2 27285 . T A 188.0 min_af_0.050000 AF=0.001946;DP=12333;DP4=9873,2431,23,1;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N28K|61|ORF6|protein_coding|CODING|GU280_gp06|1|A) +NC_045512.2 27335 . C T 427.0 min_af_0.050000 AF=0.007644;DP=4317;DP4=2285,1996,22,12;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T45I|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) +NC_045512.2 27344 . A T 816.0 min_af_0.050000 AF=0.012494;DP=4322;DP4=2322,1944,35,19;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aTa|K48I|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) +NC_045512.2 27345 . A T 813.0 min_af_0.050000 AF=0.012500;DP=4320;DP4=2323,1943,35,19;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K48N|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) +NC_045512.2 27354 . A G 859.0 min_af_0.050000 AF=0.013456;DP=4236;DP4=2370,1805,45,14;SB=24;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q51|61|ORF6|protein_coding|CODING|GU280_gp06|1|G) +NC_045512.2 27416 . C T 90.0 min_af_0.050000 AF=0.001178;DP=12734;DP4=2572,10143,2,13;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A8V|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T) +NC_045512.2 27437 . G A 143.0 min_af_0.050000 AF=0.001595;DP=12541;DP4=2423,10091,2,19;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C15Y|121|ORF7a|protein_coding|CODING|GU280_gp07|1|A) +NC_045512.2 27496 . T C 98.0 min_af_0.050000 AF=0.001317;DP=11388;DP4=1594,9778,3,12;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C35R|121|ORF7a|protein_coding|CODING|GU280_gp07|1|C) +NC_045512.2 28138 . C T 99.0 min_af_0.050000 AF=0.001215;DP=13167;DP4=11097,2039,13,5;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S82F|121|ORF8|protein_coding|CODING|GU280_gp09|1|T) +NC_045512.2 28148 . T C 83.0 min_af_0.050000 AF=0.001078;DP=12985;DP4=11170,1792,13,1;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P85|121|ORF8|protein_coding|CODING|GU280_gp09|1|C) +NC_045512.2 28342 . A G 112.0 min_af_0.050000 AF=0.001261;DP=14272;DP4=2718,11531,4,15;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S23|419|N|protein_coding|CODING|GU280_gp10|1|G) +NC_045512.2 28378 . G A 103.0 min_af_0.050000 AF=0.001371;DP=13857;DP4=2379,11440,1,18;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A35|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 28378 . G C 86.0 min_af_0.050000 AF=0.001227;DP=13857;DP4=2379,11440,5,12;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcC|A35|419|N|protein_coding|CODING|GU280_gp10|1|C) +NC_045512.2 28380 . G A 241.0 min_af_0.050000 AF=0.002170;DP=13827;DP4=2341,11452,10,21;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R36Q|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 28383 . CA C 82.0 min_af_0.050000 AF=0.000728;DP=13736;DP4=2329,11456,1,9;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K38|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00) +NC_045512.2 28774 . G A 80.0 min_af_0.050000 AF=0.001870;DP=5348;DP4=4300,1036,9,1;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L167|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 28953 . T C 88.0 min_af_0.050000 AF=0.002090;DP=5264;DP4=1078,4174,3,8;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L227S|419|N|protein_coding|CODING|GU280_gp10|1|C) +NC_045512.2 28987 . CCAA C 391.0 min_af_0.050000 AF=0.004456;DP=5611;DP4=983,4617,8,17;HRUN=2;SB=11;INDEL;EFF=CODON_DELETION(MODERATE||caa/|Q242|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME) +NC_045512.2 29029 . T C 858.0 min_af_0.050000 AF=0.004277;DP=18704;DP4=12752,5860,51,36;SB=13;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A252|419|N|protein_coding|CODING|GU280_gp10|1|C) +NC_045512.2 29039 . A T 1871.0 min_af_0.050000 AF=0.007569;DP=19026;DP4=12781,6088,89,57;SB=10;EFF=STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K256*|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29049 . G A 326.0 min_af_0.050000 AF=0.002664;DP=15392;DP4=12862,2473,41,5;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R259Q|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 29081 . GTA G 75.0 min_af_0.050000 AF=0.000573;DP=15701;DP4=12808,2895,8,1;HRUN=1;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||gta/|V270|419|N|protein_coding|CODING|GU280_gp10|1|G);LOF=(N|GU280_gp10|1|1.00) +NC_045512.2 29098 . C T 97.0 min_af_0.050000 AF=0.001203;DP=15799;DP4=12816,2957,16,3;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G275|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29132 . G A 85.0 min_af_0.050000 AF=0.001063;DP=15987;DP4=12972,2987,17,5;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G287R|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 29187 . C T 143.0 min_af_0.050000 AF=0.002863;DP=5589;DP4=3055,2517,10,6;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A305V|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29188 . A G 96.0 min_af_0.050000 AF=0.002168;DP=5536;DP4=3042,2470,8,9;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A305|419|N|protein_coding|CODING|GU280_gp10|1|G) +NC_045512.2 29195 . GC G 173.0 min_af_0.050000 AF=0.002574;DP=5439;DP4=3065,2377,8,6;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ccc/|P309|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00) +NC_045512.2 29259 . C T 80.0 min_af_0.050000 AF=0.001072;DP=15862;DP4=2960,12882,4,14;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T329M|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29322 . T C 86.0 min_af_0.050000 AF=0.001005;DP=15925;DP4=3242,12646,5,18;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V350A|419|N|protein_coding|CODING|GU280_gp10|1|C) +NC_045512.2 29348 . G A 112.0 min_af_0.050000 AF=0.001238;DP=15350;DP4=2783,12536,2,21;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A359T|419|N|protein_coding|CODING|GU280_gp10|1|A)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1085445.vcf Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,276 @@ +##fileformat=VCFv4.0 +##fileDate=20201106 +##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-14951 -o /data/dnb03/galaxy_db/job_working_directory/012/246/12246263/tmp/lofreq2_call_parallel9r7g_vq5/0.vcf.gz reads.bam +##reference=reference.fa +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> +##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> +##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant)."> +##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> +##FILTER=<ID=min_snvqual_77,Description="Minimum SNV Quality (Phred) 77"> +##FILTER=<ID=min_indelqual_64,Description="Minimum Indel Quality (Phred) 64"> +##FILTER=<ID=min_snvqual_81,Description="Minimum SNV Quality (Phred) 81"> +##FILTER=<ID=min_indelqual_67,Description="Minimum Indel Quality (Phred) 67"> +##FILTER=<ID=min_af_0.050000,Description="Minimum allele frequency 0.050000"> +##FILTER=<ID=min_dp_5,Description="Minimum Coverage 5"> +##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000"> +##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani" +##SnpEffCmd="SnpEff -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -stats /data/dnb03/galaxy_db/job_working_directory/012/246/12246330/outputs/galaxy_dataset_12727ea3-b173-47f2-a640-8b761bc6dbc9.dat NC_045512.2 /data/dnb03/galaxy_db/files/6/d/3/dataset_6d370681-43dc-4f44-ad01-c8a251815384.dat " +##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype [ | ERRORS | WARNINGS ] )' "> +##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +#CHROM POS ID REF ALT QUAL FILTER INFO +NC_045512.2 241 . C T 49314.0 PASS AF=0.991443;DP=8180;DP4=12,7,3967,4190;SB=5 +NC_045512.2 361 . A G 108.0 min_af_0.050000 AF=0.000916;DP=24022;DP4=10476,13511,11,15;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G32|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G32|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G32|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G32|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G) +NC_045512.2 385 . A G 83.0 min_af_0.050000 AF=0.000852;DP=23474;DP4=10007,13442,12,11;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S40|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S40|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S40|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S40|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G) +NC_045512.2 443 . GT G 392.0 min_af_0.050000 AF=0.002591;DP=11579;DP4=8340,3245,18,12;HRUN=4;SB=8;INDEL;EFF=FRAME_SHIFT(HIGH||ttg/|L61|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 507 . ATGGTCATGTTATGGT A 231.0 min_af_0.050000 AF=0.002668;DP=5998;DP4=3100,2886,12,4;HRUN=1;SB=10;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatggttgag/gag|GHVMVE82E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatggttgag/gag|GHVMVE82E|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatggttgag/gag|GHVMVE82E|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatggttgag/gag|GHVMVE82E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME) +NC_045512.2 509 . GGTCATGTTATGGTT G 80.0 min_af_0.050000 AF=0.001176;DP=5951;DP4=3124,2862,7,0;HRUN=2;SB=17;INDEL;EFF=FRAME_SHIFT(HIGH||ggtcatgttatggttgag/|GHVMVE82|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggtcatgttatggttgag/|GHVMVE82|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggtcatgttatggttgag/|GHVMVE82|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggtcatgttatggttgag/|GHVMVE82|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 509 . GGTCATGTT G 95.0 min_af_0.050000 AF=0.001344;DP=5951;DP4=3124,2862,3,5;HRUN=2;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||ggtcatgtt/|GHV82|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),FRAME_SHIFT(HIGH||ggtcatgtt/|GHV82|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||ggtcatgtt/|GHV82|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||ggtcatgtt/|GHV82|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 514 . TGTTATG T 95.0 min_af_0.050000 AF=0.001356;DP=5899;DP4=3143,2829,3,5;HRUN=1;SB=3;INDEL;EFF=CODON_DELETION(MODERATE||atggtt/|MV85|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||atggtt/|MV85|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||atggtt/|MV85|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||atggtt/|MV85|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME) +NC_045512.2 518 . ATGGTT A 79.0 min_af_0.050000 AF=0.001180;DP=5933;DP4=3134,2801,3,4;HRUN=1;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||atggtt/|MV85|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),FRAME_SHIFT(HIGH||atggtt/|MV85|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||atggtt/|MV85|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||atggtt/|MV85|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 558 . G T 263.0 min_af_0.050000 AF=0.004646;DP=5596;DP4=3200,2366,18,9;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G98V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G98V|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G98V|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G98V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T) +NC_045512.2 601 . C T 114.0 min_af_0.050000 AF=0.001426;DP=12622;DP4=3414,9185,8,11;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G112|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G112|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G112|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G112|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T) +NC_045512.2 683 . CTA C 109.0 min_af_0.050000 AF=0.000870;DP=12642;DP4=3760,8924,6,5;HRUN=1;SB=10;INDEL;EFF=FRAME_SHIFT(HIGH||cta/|L140|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),FRAME_SHIFT(HIGH||cta/|L140|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|C|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||cta/|L140|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|C|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||cta/|L140|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 685 . AAAGTCATTT A 721.0 min_af_0.050000 AF=0.003737;DP=12578;DP4=3649,8908,17,30;HRUN=3;SB=4;INDEL;EFF=CODON_DELETION(MODERATE||aagtcattt/|KSF141|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_DELETION(MODERATE||aagtcattt/|KSF141|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_DELETION(MODERATE||aagtcattt/|KSF141|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_DELETION(MODERATE||aagtcattt/|KSF141|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A) +NC_045512.2 891 . G A 82.0 min_af_0.050000 AF=0.003096;DP=2584;DP4=700,1876,4,4;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G209D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G209D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G29D|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G29D|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1001 . GA G 70.0 min_af_0.050000 AF=0.000521;DP=19212;DP4=14170,5050,7,3;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K247|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K247|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K67|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K67|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) +NC_045512.2 1011 . ATG A 158.0 min_af_0.050000 AF=0.000902;DP=17731;DP4=14217,3504,14,2;HRUN=1;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||tatgaa/|YE249|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),FRAME_SHIFT(HIGH||tatgaa/|YE249|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),FRAME_SHIFT(HIGH||tatgaa/|YE69|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||tatgaa/|YE69|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.11) +NC_045512.2 1018 . G A 194.0 min_af_0.050000 AF=0.001555;DP=18008;DP4=14268,3704,24,6;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L251|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L251|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L71|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L71|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1019 . C T 96.0 min_af_0.050000 AF=0.000990;DP=18175;DP4=14292,3861,14,5;SB=2;EFF=STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q252*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q252*|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q72*|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q72*|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04) +NC_045512.2 1059 . C T 49314.0 PASS AF=0.914482;DP=18230;DP4=1138,343,12822,3919;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T265I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T265I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T85I|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T85I|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1115 . A T 112.0 min_af_0.050000 AF=0.002090;DP=6697;DP4=2661,4022,1,13;SB=19;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I284F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I284F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I104F|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I104F|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1140 . A G 82.0 min_af_0.050000 AF=0.001915;DP=6788;DP4=2923,3852,5,8;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K292R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K292R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K112R|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K112R|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1288 . C T 96.0 min_af_0.050000 AF=0.001212;DP=15681;DP4=3701,11913,4,57;SB=31;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C341|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C341|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C161|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C161|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1644 . A C 204.0 min_af_0.050000 AF=0.001874;DP=14945;DP4=11652,3256,18,14;SB=22;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N460T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N460T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N280T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N280T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1647 . T A 204.0 min_af_0.050000 AF=0.001794;DP=15048;DP4=11650,3368,14,14;SB=26;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I461N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I461N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I281N|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I281N|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1656 . T A 169.0 min_af_0.050000 AF=0.001647;DP=15179;DP4=11625,3520,18,12;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V464D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V464D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V284D|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V284D|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1659 . G T 171.0 min_af_0.050000 AF=0.001899;DP=15272;DP4=11693,3542,22,12;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G465V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G465V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G285V|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G285V|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1698 . C T 85.0 min_af_0.050000 AF=0.001095;DP=15526;DP4=11739,3762,12,7;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A478V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A478V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A298V|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A298V|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1701 . CT C 201.0 min_af_0.050000 AF=0.001361;DP=15428;DP4=11734,3700,17,4;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||tct/|S481|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tct/|S481|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tct/|S301|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tct/|S301|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 1702 . T C 336.0 min_af_0.050000 AF=0.002654;DP=15449;DP4=11702,3680,34,10;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S479|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S479|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S299|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S299|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1710 . C T 131.0 min_af_0.050000 AF=0.001431;DP=15372;DP4=11672,3674,11,12;SB=23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A482V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A482V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A302V|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A302V|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1733 . A G 97.0 min_af_0.050000 AF=0.001812;DP=7174;DP4=3582,3573,16,1;SB=35;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T490A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T490A|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T310A|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T310A|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1914 . G A 164.0 min_af_0.050000 AF=0.001604;DP=14959;DP4=3270,11663,2,22;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R550H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R550H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R370H|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R370H|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1928 . G A 122.0 min_af_0.050000 AF=0.001310;DP=14507;DP4=2942,11544,2,17;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A555T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A555T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A375T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A375T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 2240 . A T 102.0 min_af_0.050000 AF=0.005411;DP=1848;DP4=440,1398,1,9;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I659F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I659F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I479F|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I479F|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 2371 . C A 84.0 min_af_0.050000 AF=0.033898;DP=118;DP4=57,56,3,2;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A702|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A702|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A522|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A522|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 3037 . C T 49314.0 PASS AF=0.989605;DP=1924;DP4=1,3,905,1013;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 3178 . T C 85.0 min_af_0.050000 AF=0.001409;DP=9934;DP4=6039,3875,10,7;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P971|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P971|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P153|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P153|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 3290 . C G 201.0 min_af_0.050000 AF=0.002822;DP=7796;DP4=6032,1737,15,7;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q1009E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q1009E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q191E|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q191E|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 3373 . C A 4347.0 PASS AF=0.062157;DP=3282;DP4=1695,1380,116,90;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D1036E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D1036E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D218E|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D218E|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 3412 . TA T 167.0 min_af_0.050000 AF=0.001903;DP=7881;DP4=1821,6068,4,11;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K1051|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K1051|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K233|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K233|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 3832 . CT C 207.0 min_af_0.050000 AF=0.003618;DP=4146;DP4=3478,655,12,3;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttg/|L1191|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L1191|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L373|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L373|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 4142 . G A 162.0 min_af_0.050000 AF=0.001370;DP=21166;DP4=14320,6812,14,19;SB=23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E1293K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E1293K|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E475K|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E475K|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4179 . A G 90.0 min_af_0.050000 AF=0.001176;DP=19554;DP4=14327,5191,20,8;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K1305R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K1305R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K487R|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K487R|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4289 . G A 89.0 min_af_0.050000 AF=0.001013;DP=19750;DP4=5529,14191,8,13;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1342T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1342T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A524T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A524T|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4308 . A G 267.0 min_af_0.050000 AF=0.001968;DP=20834;DP4=5011,15773,12,32;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K1348R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K1348R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K530R|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K530R|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5291 . CT C 168.0 min_af_0.050000 AF=0.001809;DP=7188;DP4=5641,1540,12,1;HRUN=2;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||ctt/|L1676|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/|L1676|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/|L858|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/|L858|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 5387 . G A 82.0 min_af_0.050000 AF=0.001671;DP=6582;DP4=4204,2365,8,3;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A1708T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A1708T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A890T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A890T|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5400 . C T 116.0 min_af_0.050000 AF=0.002168;DP=6458;DP4=4180,2261,9,6;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1712V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1712V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A894V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A894V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5743 . G C 265.0 min_af_0.050000 AF=0.005125;DP=4683;DP4=2467,2189,5,19;SB=27;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1826D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1826D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1008D|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1008D|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5744 . T C 406.0 min_af_0.050000 AF=0.007072;DP=4666;DP4=2466,2162,10,26;SB=26;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1827H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1827H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1009H|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1009H|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5765 . G A 192.0 min_af_0.050000 AF=0.004055;DP=4686;DP4=2625,2040,4,16;SB=29;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1834S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1834S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1016S|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1016S|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5766 . G C 133.0 min_af_0.050000 AF=0.003178;DP=4720;DP4=2667,2035,3,12;SB=21;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G1834A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G1834A|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G1016A|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G1016A|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6181 . TA T 74.0 min_af_0.050000 AF=0.000612;DP=14709;DP4=2144,12612,0,9;HRUN=3;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K1973|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1973|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1155|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1155|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 6242 . C T 165.0 min_af_0.050000 AF=0.000825;DP=46066;DP4=29941,16067,31,16;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1993Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1993Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1175Y|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1175Y|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6254 . G A 105.0 min_af_0.050000 AF=0.000684;DP=39491;DP4=30022,9423,21,10;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1997T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1997T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1179T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1179T|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6271 . G A 379.0 min_af_0.050000 AF=0.001604;DP=39896;DP4=29246,10561,43,29;SB=19;EFF=SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T2002|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T2002|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1184|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1184|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6364 . G A 108.0 min_af_0.050000 AF=0.001237;DP=16980;DP4=8010,8945,14,9;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A2033|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A2033|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A1215|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A1215|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6396 . TA T 87.0 min_af_0.050000 AF=0.000649;DP=18497;DP4=8545,10129,7,5;HRUN=4;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K2045|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K2045|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1227|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1227|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 6402 . C T 109.0 min_af_0.050000 AF=0.000771;DP=36334;DP4=8494,27803,7,23;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P2046L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P2046L|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P1228L|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P1228L|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6409 . T C 104.0 min_af_0.050000 AF=0.000721;DP=36080;DP4=8420,27622,5,22;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S2048|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S2048|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1230|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1230|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 7431 . CATTTT C 70.0 min_af_0.050000 AF=0.004202;DP=952;DP4=599,351,2,2;HRUN=1;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||ttttattat/|FYY2390|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttttattat/|FYY2390|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttttattat/|FYY1572|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttttattat/|FYY1572|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 7736 . G A 87.0 min_af_0.050000 AF=0.001450;DP=9654;DP4=7167,2470,12,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V2491I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V2491I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1673I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1673I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 7738 . T C 96.0 min_af_0.050000 AF=0.001449;DP=9661;DP4=7170,2476,11,4;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V2491|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V2491|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V1673|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V1673|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 7771 . T G 119.0 min_af_0.050000 AF=0.001861;DP=9671;DP4=7169,2479,8,10;SB=19;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caG|H2502Q|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caG|H2502Q|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caG|H1684Q|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caG|H1684Q|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 7889 . GT G 495.0 min_af_0.050000 AF=0.003791;DP=9496;DP4=2286,7193,8,28;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F2543|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F2543|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F1725|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F1725|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 8927 . GT G 77.0 min_af_0.050000 AF=0.001225;DP=6529;DP4=5082,1441,6,2;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F2889|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F2889|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F126|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F126|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 9014 . G A 94.0 min_af_0.050000 AF=0.001833;DP=7092;DP4=5255,1822,9,4;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A2917T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A2917T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A154T|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A154T|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 9479 . G T 578.0 min_af_0.050000 AF=0.027073;DP=1182;DP4=216,934,17,15;SB=47;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Tgt|G3072C|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Tgt|G3072C|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Tgt|G309C|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Tgt|G309C|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 9656 . A G 85.0 min_af_0.050000 AF=0.002371;DP=4218;DP4=1823,2383,10,0;SB=36;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M3131V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M3131V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M368V|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M368V|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 9737 . A AG 93.0 min_af_0.050000 AF=0.000941;DP=9561;DP4=2070,7513,4,5;HRUN=1;SB=9;INDEL;EFF=FRAME_SHIFT(HIGH||agt/agGt|S3158R?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|AG|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||agt/agGt|S3158R?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|AG|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||agt/agGt|S395R?|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|AG|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||agt/agGt|S395R?|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|AG|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 9919 . T C 86.0 min_af_0.050000 AF=0.008837;DP=679;DP4=478,194,3,3;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S3218|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S3218|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S455|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S455|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 10615 . C T 116.0 min_af_0.050000 AF=0.002812;DP=4623;DP4=1510,3095,5,9;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3450|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3450|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D187|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D187|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 10635 . C T 136.0 min_af_0.050000 AF=0.002999;DP=4668;DP4=1550,3104,5,9;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3457V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3457V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A194V|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A194V|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 10874 . A T 122.0 min_af_0.050000 AF=0.007206;DP=1249;DP4=654,586,4,5;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N3537Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N3537Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N274Y|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N274Y|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11082 . TG T 110.0 min_af_0.050000 AF=0.000734;DP=16355;DP4=12351,4023,10,2;HRUN=1;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttg/|L3606|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),FRAME_SHIFT(HIGH||ttg/|L3606|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),FRAME_SHIFT(HIGH||ttg/|L37|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||ttg/|L37|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 11083 . G T 328.0 min_af_0.050000 AF=0.003159;DP=16459;DP4=12330,4055,43,15;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L3606F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L3606F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L37F|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L37F|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11250 . G A 84.0 min_af_0.050000 AF=0.000966;DP=17602;DP4=4658,12920,6,11;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R3662H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R3662H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R93H|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R93H|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11292 . GT G 105.0 min_af_0.050000 AF=0.000711;DP=18275;DP4=5121,13165,5,8;HRUN=4;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F3677|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F3677|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F108|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F108|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 11654 . T C 101.0 min_af_0.050000 AF=0.001376;DP=12355;DP4=6380,5954,10,7;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F3797L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F3797L|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F228L|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F228L|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11895 . A G 117.0 min_af_0.050000 AF=0.001058;DP=21736;DP4=13835,7875,13,11;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q3877R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q3877R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q18R|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q18R|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11952 . A T 108.0 min_af_0.050000 AF=0.001249;DP=17618;DP4=13412,4175,18,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aTt|N3896I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aTt|N3896I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aTt|N37I|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aTt|N37I|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12031 . G A 88.0 min_af_0.050000 AF=0.001927;DP=8304;DP4=4111,4170,10,7;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q3922|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q3922|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q63|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q63|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12035 . G A 91.0 min_af_0.050000 AF=0.001697;DP=8249;DP4=4097,4133,7,9;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3924T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3924T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A65T|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A65T|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12128 . G A 124.0 min_af_0.050000 AF=0.001125;DP=20441;DP4=4710,15706,10,14;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A3955T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A3955T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A13T|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A13T|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12143 . G A 171.0 min_af_0.050000 AF=0.001269;DP=22057;DP4=6298,15713,9,20;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3960T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3960T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A18T|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A18T|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12164 . G T 158.0 min_af_0.050000 AF=0.001229;DP=21965;DP4=6177,15735,10,23;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A3967S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A3967S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A25S|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A25S|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12201 . A G 203.0 min_af_0.050000 AF=0.001756;DP=20503;DP4=5036,15425,12,27;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K3979R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K3979R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K37R|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K37R|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12458 . A G 2325.0 min_af_0.050000 AF=0.010507;DP=15038;DP4=11454,3422,135,23;SB=19;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T4065A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T4065A|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T123A|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T123A|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12673 . T C 83.0 min_af_0.050000 AF=0.001026;DP=14614;DP4=3924,10673,5,11;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4136|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4136|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A194|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A194|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12684 . A G 90.0 min_af_0.050000 AF=0.001091;DP=14670;DP4=3905,10744,3,13;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q4140R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q4140R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|cAg/cGg|Q198R|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|cAg/cGg|Q198R|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12703 . T C 99.0 min_af_0.050000 AF=0.001164;DP=14610;DP4=3877,10708,6,16;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4146|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4146|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P6|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P6|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13006 . T C 100.0 min_af_0.050000 AF=0.001091;DP=18324;DP4=4970,13320,5,18;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4247|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4247|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A107|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A107|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13034 . G A 287.0 min_af_0.050000 AF=0.001172;DP=43512;DP4=25678,17773,36,17;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4257T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4257T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13039 . A G 153.0 min_af_0.050000 AF=0.000801;DP=43670;DP4=25606,18020,23,15;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T4258|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T4258|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T5|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T5|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13049 . G A 126.0 min_af_0.050000 AF=0.000745;DP=44275;DP4=25781,18447,22,16;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4262T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4262T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A9T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A9T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13050 . C T 160.0 min_af_0.050000 AF=0.000857;DP=44323;DP4=25765,18501,28,14;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A4262V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A4262V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A9V|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A9V|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13123 . TG T 90.0 min_af_0.050000 AF=0.000496;DP=32271;DP4=23537,8806,12,4;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||gga/|G4288|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G4288|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G35|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G35|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) +NC_045512.2 13126 . G T 894.0 min_af_0.050000 AF=0.003763;DP=32684;DP4=23617,8932,96,30;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggG/ggT|G4287|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggT|G4287|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggT|G34|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggT|G34|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13129 . A G 415.0 min_af_0.050000 AF=0.002114;DP=32636;DP4=23626,8909,60,24;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13142 . AATT A 68.0 min_af_0.050000 AF=0.000345;DP=31908;DP4=23436,8544,7,4;HRUN=2;SB=3;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgt/agt|NC4293S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgt/agt|NC4293S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgt/agt|NC40S|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgt/agt|NC40S|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13178 . G A 92.0 min_af_0.050000 AF=0.001099;DP=15464;DP4=7168,8274,7,12;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G4305S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G4305S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G52S|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G52S|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13184 . G A 88.0 min_af_0.050000 AF=0.001085;DP=15669;DP4=7536,8107,10,8;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4307T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4307T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A54T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A54T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13235 . G A 184.0 min_af_0.050000 AF=0.001314;DP=30447;DP4=8620,21776,11,31;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4324T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4324T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A71T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A71T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13240 . G A 120.0 min_af_0.050000 AF=0.001047;DP=30554;DP4=8647,21862,13,25;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S4325|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S4325|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S72|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S72|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13255 . C T 121.0 min_af_0.050000 AF=0.000922;DP=32523;DP4=8871,23617,11,19;SB=5;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C4330|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C4330|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C77|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C77|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13257 . G A 103.0 min_af_0.050000 AF=0.000795;DP=32720;DP4=8969,23719,5,23;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R4331H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R4331H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R78H|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R78H|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13299 . TA T 67.0 min_af_0.050000 AF=0.000373;DP=32129;DP4=8835,23401,3,9;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K4346|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K4346|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K93|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K93|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) +NC_045512.2 13345 . T C 114.0 min_af_0.050000 AF=0.000845;DP=34302;DP4=11365,22885,12,23;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4360|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4360|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P107|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P107|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13385 . G A 203.0 min_af_0.050000 AF=0.003101;DP=9673;DP4=7564,2070,23,10;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G4374S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G4374S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G121S|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G121S|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13482 . A G 84.0 min_af_0.050000 AF=0.002138;DP=5145;DP4=2849,2284,8,3;SB=4;EFF=SPLICE_SITE_REGION+SYNONYMOUS_STOP(LOW|SILENT|tAa/tGa|*4406|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V4406|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V14|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13541 . CT C 128.0 min_af_0.050000 AF=0.001323;DP=9073;DP4=2350,6760,4,8;HRUN=4;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F4427|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F35|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.04) +NC_045512.2 13565 . T G 710.0 min_af_0.050000 AF=0.006207;DP=9345;DP4=2347,6927,31,27;SB=52;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gGa|V4434G|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gGa|V42G|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13571 . G T 498.0 min_af_0.050000 AF=0.004930;DP=9533;DP4=2456,7025,10,39;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G4436V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G44V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13586 . TA T 114.0 min_af_0.050000 AF=0.001250;DP=9600;DP4=2526,7104,3,9;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||act/|T4443|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||act/|T51|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 13729 . G A 97.0 min_af_0.050000 AF=0.000758;DP=31659;DP4=23911,7707,19,7;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A4489T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A97T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13982 . G A 334.0 min_af_0.050000 AF=0.003336;DP=13191;DP4=10186,2952,21,25;SB=55;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R4573H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R181H|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14197 . G A 131.0 min_af_0.050000 AF=0.001509;DP=12592;DP4=2965,9602,4,17;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4645T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A253T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14408 . C T 49314.0 PASS AF=0.993579;DP=1869;DP4=2,1,961,905;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4715L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P323L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14625 . CT C 95.0 min_af_0.050000 AF=0.000978;DP=10228;DP4=7598,2681,7,3;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||tca/|S4789|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tca/|S397|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 14638 . G A 81.0 min_af_0.050000 AF=0.001254;DP=10364;DP4=7602,2745,9,5;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4792T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A400T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15380 . G T 19339.0 PASS AF=0.137502;DP=5629;DP4=2428,2416,397,383;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aTc|S5039I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aTc|S647I|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15481 . T C 525.0 min_af_0.050000 AF=0.004225;DP=12307;DP4=3137,9071,51,40;SB=87;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S5073P|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S681P|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15537 . T C 82.0 min_af_0.050000 AF=0.000714;DP=32206;DP4=19463,12697,24,11;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A5091|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A699|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15602 . G A 81.0 min_af_0.050000 AF=0.000869;DP=25304;DP4=18787,6490,16,6;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R5113H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R721H|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15673 . T G 170.0 min_af_0.050000;sb_fdr AF=0.002959;DP=11154;DP4=5550,5555,29,5;SB=44;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Gtt|F5137V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Gtt|F745V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15682 . T A 3591.0 min_af_0.050000 AF=0.019897;DP=11057;DP4=5644,5185,123,101;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y5140N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y748N|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15685 . T A 3576.0 min_af_0.050000 AF=0.019571;DP=11088;DP4=5677,5189,119,98;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L5141M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L749M|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15784 . T TGAC 112.0 min_af_0.050000 AF=0.000564;DP=24832;DP4=6387,18537,7,7;HRUN=3;SB=12;INDEL;EFF=STOP_GAINED+CODON_CHANGE_PLUS_CODON_INSERTION(HIGH||ttt/tGACtt|F5174*L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|TGAC),STOP_GAINED+CODON_CHANGE_PLUS_CODON_INSERTION(HIGH||ttt/tGACtt|F782*L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|TGAC|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15788 . AGTC A 113.0 min_af_0.050000 AF=0.000570;DP=24581;DP4=6120,18483,7,7;HRUN=1;SB=12;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aagtca/aaa|KS5175K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aagtca/aaa|KS783K|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 16946 . C T 81.0 min_af_0.050000 AF=0.002242;DP=4461;DP4=1946,2504,5,6;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A5561V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A237V|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 17035 . G A 130.0 min_af_0.050000 AF=0.002105;DP=8076;DP4=2373,5684,6,12;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A5591T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A267T|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 17146 . A G 124.0 min_af_0.050000 AF=0.001762;DP=11915;DP4=8858,3024,17,7;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5628V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I304V|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 17200 . TTAAAA T 215.0 min_af_0.050000 AF=0.001499;DP=12007;DP4=8894,3153,15,3;HRUN=2;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||aaatat/|KY5647|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaatat/|KY323|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 17410 . C T 89.0 min_af_0.050000 AF=0.001226;DP=13051;DP4=3103,9927,5,12;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5716C|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R392C|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 18687 . CT C 125.0 min_af_0.050000 AF=0.001021;DP=13716;DP4=10356,3385,9,5;HRUN=4;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||tcc/|S6143|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tcc/|S218|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 18839 . C T 87.0 min_af_0.050000 AF=0.001144;DP=13109;DP4=3502,9590,6,9;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A6192V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A267V|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19029 . C T 142.0 min_af_0.050000 AF=0.001333;DP=18002;DP4=13296,4678,17,7;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H6255|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H330|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19132 . G T 183.0 min_af_0.050000 AF=0.002631;DP=7981;DP4=4498,3460,10,12;SB=4;EFF=STOP_GAINED(HIGH|NONSENSE|Gaa/Taa|E6290*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),STOP_GAINED(HIGH|NONSENSE|Gaa/Taa|E365*|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19137 . A C 139.0 min_af_0.050000 AF=0.002242;DP=8029;DP4=4529,3481,8,10;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttA/ttC|L6291F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttA/ttC|L366F|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19173 . A G 184.0 min_af_0.050000 AF=0.001475;DP=18300;DP4=4405,13862,8,20;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T6303|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T378|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19199 . G A 95.0 min_af_0.050000 AF=0.000992;DP=18154;DP4=4265,13867,5,14;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C6312Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C387Y|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19554 . CT C 88.0 min_af_0.050000 AF=0.002555;DP=2348;DP4=169,2178,0,6;HRUN=3;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F6431|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F506|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.04) +NC_045512.2 19804 . A G 95.0 min_af_0.050000 AF=0.001057;DP=17023;DP4=4133,12868,6,14;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N6514D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N62D|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 20555 . C T 1517.0 min_af_0.050000 AF=0.008538;DP=12766;DP4=9871,2780,90,22;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S6764F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S312F|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 20769 . TA T 71.0 min_af_0.050000 AF=0.000640;DP=12508;DP4=3063,9486,3,5;HRUN=3;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K6836|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K38|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.04) +NC_045512.2 20791 . G A 100.0 min_af_0.050000 AF=0.001350;DP=14075;DP4=2871,11181,6,16;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A6843T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A45T|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 21066 . TA T 267.0 min_af_0.050000 AF=0.001799;DP=13898;DP4=3162,10753,8,17;HRUN=5;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||aat/|N6936|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aat/|N138|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.04) +NC_045512.2 21093 . TA T 69.0 min_af_0.050000 AF=0.000600;DP=13336;DP4=2749,10687,2,6;HRUN=3;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K6944|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K146|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.04) +NC_045512.2 21123 . G T 2708.0 min_af_0.050000 AF=0.013197;DP=13412;DP4=3026,10193,36,152;SB=5;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggG/ggT|G6953|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggT|G155|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 21204 . G T 1022.0 min_af_0.050000 AF=0.041982;DP=1191;DP4=795,343,25,27;SB=27;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K6980N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K182N|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 21650 . A C 117.0 min_af_0.050000 AF=0.004405;DP=2270;DP4=628,1631,2,8;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Cat|N30H|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 21656 . TTCAC T 72.0 min_af_0.050000 AF=0.002225;DP=2247;DP4=622,1639,2,3;HRUN=3;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||ttcaca/|FT32|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 21736 . CT C 78.0 min_af_0.050000 AF=0.000985;DP=8122;DP4=6241,1886,6,2;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||tcc/|S60|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME) +NC_045512.2 21954 . G A 81.0 min_af_0.050000 AF=0.001578;DP=6970;DP4=1556,5401,2,9;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C131Y|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 22000 . CA C 164.0 min_af_0.050000 AF=0.001817;DP=8255;DP4=2894,5378,9,6;HRUN=5;SB=12;INDEL;EFF=FRAME_SHIFT(HIGH||aac/|N148|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 22091 . A G 248.0 min_af_0.050000 AF=0.006641;DP=2861;DP4=2126,714,18,1;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M177V|1273|S|protein_coding|CODING|GU280_gp02|1|G) +NC_045512.2 22120 . CA C 69.0 min_af_0.050000 AF=0.003159;DP=1583;DP4=970,695,1,4;HRUN=5;SB=7;INDEL;EFF=FRAME_SHIFT(HIGH||aat/|N188|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 22583 . GTTT G 87.0 min_af_0.050000 AF=0.000843;DP=13055;DP4=10169,2877,8,3;HRUN=5;SB=1;INDEL;EFF=CODON_DELETION(MODERATE||ttt/|F342|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME) +NC_045512.2 22643 . T A 561.0 min_af_0.050000 AF=0.003894;DP=13611;DP4=10284,3268,43,11;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C361S|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 22644 . G C 533.0 min_af_0.050000 AF=0.003793;DP=13710;DP4=10293,3357,41,11;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C361S|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 22645 . T A 522.0 min_af_0.050000 AF=0.003723;DP=13699;DP4=10277,3356,44,11;SB=2;EFF=STOP_GAINED(HIGH|NONSENSE|tgT/tgA|C361*|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 22851 . C T 115.0 min_af_0.050000 AF=0.001412;DP=12041;DP4=3221,8772,5,33;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T430I|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 22858 . C T 81.0 min_af_0.050000 AF=0.001258;DP=11921;DP4=3141,8751,5,11;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C432|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 23131 . TG T 92.0 min_af_0.050000 AF=0.001755;DP=3989;DP4=819,3176,0,7;HRUN=1;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||gtt/|V524|1273|S|protein_coding|CODING|GU280_gp02|1|T);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 23132 . GT G 125.0 min_af_0.050000 AF=0.002191;DP=4108;DP4=817,3296,0,9;HRUN=3;SB=6;INDEL;EFF=FRAME_SHIFT(HIGH||tgt/|C525|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 23403 . A G 49314.0 PASS AF=0.991574;DP=16497;DP4=5,22,4298,12165;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G) +NC_045512.2 23417 . G T 370.0 min_af_0.050000 AF=0.002551;DP=16465;DP4=4287,12132,12,30;SB=1;EFF=STOP_GAINED(HIGH|NONSENSE|Gaa/Taa|E619*|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 23554 . ACCCATTGGTGCAGGTATATGCGCTAGTT A 194.0 min_af_0.050000 AF=0.002880;DP=4514;DP4=3258,1249,11,2;HRUN=3;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||cccattggtgcaggtatatgcgctagttat/|PIGAGICASY665|1273|S|protein_coding|CODING|GU280_gp02|1|A);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 23582 . TATCAGACTCAGACTA T 519.0 min_af_0.050000 AF=0.006436;DP=4506;DP4=3258,1232,14,15;HRUN=1;SB=22;INDEL;EFF=CODON_DELETION(MODERATE||cagactcagactaat/|QTQTN675|1273|S|protein_coding|CODING|GU280_gp02|1|T|INFO_REALIGN_3_PRIME) +NC_045512.2 24728 . G A 138.0 min_af_0.050000 AF=0.001075;DP=23260;DP4=18198,5032,20,6;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1056T|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 24729 . C T 267.0 min_af_0.050000 AF=0.001633;DP=23275;DP4=18189,5042,31,9;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1056V|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 24770 . G A 85.0 min_af_0.050000 AF=0.000776;DP=24482;DP4=18807,5645,16,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1070T|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 24771 . C T 100.0 min_af_0.050000 AF=0.000857;DP=24506;DP4=18807,5671,17,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1070V|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 24794 . G A 173.0 min_af_0.050000 AF=0.001191;DP=25181;DP4=18729,6412,23,8;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A1078T|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 24910 . TAC T 77.0 min_af_0.050000 AF=0.000771;DP=10375;DP4=5736,4681,6,2;HRUN=1;SB=5;INDEL;EFF=FRAME_SHIFT(HIGH||aca/|T1117|1273|S|protein_coding|CODING|GU280_gp02|1|T|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 24933 . G T 547.0 min_af_0.050000 AF=0.002715;DP=23942;DP4=5894,17971,24,44;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G1124V|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 24938 . T C 90.0 min_af_0.050000 AF=0.000836;DP=23912;DP4=5888,17993,5,17;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C1126R|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 24942 . A T 433.0 min_af_0.050000 AF=0.002206;DP=24029;DP4=5968,18000,7,48;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D1127V|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 24986 . C T 213.0 min_af_0.050000 AF=0.001391;DP=23728;DP4=5830,17860,9,24;SB=1;EFF=STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q1142*|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 25344 . C T 81.0 min_af_0.050000;sb_fdr AF=0.002408;DP=11212;DP4=8717,2463,4,24;SB=118;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S1261F|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 25563 . G T 49314.0 PASS AF=0.910164;DP=12456;DP4=238,777,2686,8750;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q57H|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) +NC_045512.2 25567 . G A 86.0 min_af_0.050000 AF=0.001207;DP=12424;DP4=2908,9492,5,12;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A59T|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) +NC_045512.2 25572 . CA C 112.0 min_af_0.050000 AF=0.000961;DP=12491;DP4=2976,9571,1,11;HRUN=4;SB=5;INDEL;EFF=FRAME_SHIFT(HIGH||atc/|I62|275|ORF3a|protein_coding|CODING|GU280_gp03|1|C|INFO_REALIGN_3_PRIME);LOF=(ORF3a|GU280_gp03|1|1.00) +NC_045512.2 25635 . C T 95.0 min_af_0.050000 AF=0.001259;DP=11913;DP4=2737,9155,4,11;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C81|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) +NC_045512.2 25646 . T G 88.0 min_af_0.050000;sb_fdr AF=0.001532;DP=11748;DP4=2658,9069,16,2;SB=83;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tGg|L85W|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) +NC_045512.2 25797 . CA C 93.0 min_af_0.050000 AF=0.004626;DP=1297;DP4=521,784,1,5;HRUN=5;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||aac/|N137|275|ORF3a|protein_coding|CODING|GU280_gp03|1|C|INFO_REALIGN_3_PRIME);LOF=(ORF3a|GU280_gp03|1|1.00) +NC_045512.2 26042 . C T 1956.0 min_af_0.050000 AF=0.008189;DP=17706;DP4=12836,4716,99,50;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T217I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) +NC_045512.2 26044 . C G 1842.0 min_af_0.050000 AF=0.007844;DP=17592;DP4=12777,4670,91,48;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q218E|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) +NC_045512.2 26046 . A G 1895.0 min_af_0.050000 AF=0.008153;DP=17662;DP4=12782,4734,95,51;SB=14;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q218|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) +NC_045512.2 26057 . A C 226.0 min_af_0.050000 AF=0.003504;DP=11131;DP4=6545,4539,21,19;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gCc|D222A|275|ORF3a|protein_coding|CODING|GU280_gp03|1|C) +NC_045512.2 26089 . T A 325.0 min_af_0.050000 AF=0.003996;DP=7758;DP4=3605,4118,5,28;SB=35;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Aac|Y233N|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) +NC_045512.2 26103 . T A 508.0 min_af_0.050000 AF=0.005526;DP=7963;DP4=3881,4036,34,10;SB=36;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V237|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) +NC_045512.2 26157 . TGTTA T 86.0 min_af_0.050000 AF=0.001022;DP=7827;DP4=4500,3335,7,1;HRUN=1;SB=8;INDEL;EFF=FRAME_SHIFT(HIGH||gttaat/|VN256|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T);LOF=(ORF3a|GU280_gp03|1|1.00) +NC_045512.2 26189 . A G 161.0 min_af_0.050000 AF=0.001616;DP=17322;DP4=4576,12716,9,21;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E266G|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) +NC_045512.2 26542 . C A 369.0 min_af_0.050000 AF=0.006926;DP=4043;DP4=233,3778,5,23;SB=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aAt|T7N|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 26545 . T G 1128.0 min_af_0.050000 AF=0.004540;DP=24230;DP4=20240,3866,88,26;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aGt|I8S|222|M|protein_coding|CODING|GU280_gp05|1|G) +NC_045512.2 26554 . A G 296.0 min_af_0.050000 AF=0.001728;DP=24881;DP4=20503,4324,36,11;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E11G|222|M|protein_coding|CODING|GU280_gp05|1|G) +NC_045512.2 26566 . A G 125.0 min_af_0.050000 AF=0.001328;DP=25594;DP4=20737,4806,27,9;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K15R|222|M|protein_coding|CODING|GU280_gp05|1|G) +NC_045512.2 26573 . TGAACAATGGAACCTAGTAATAGGTTTCCTA T 159.0 min_af_0.050000 AF=0.000710;DP=25348;DP4=20879,4448,14,4;HRUN=1;SB=2;INDEL;EFF=CODON_DELETION(MODERATE||gaacaatggaacctagtaataggtttccta/|EQWNLVIGFL18|222|M|protein_coding|CODING|GU280_gp05|1|T) +NC_045512.2 26574 . GAACAATGGAACCTAGTAATAGGTTTCCTA G 99.0 min_af_0.050000 AF=0.000510;DP=25466;DP4=20936,4518,12,1;HRUN=2;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||gaacaatggaacctagtaataggtttccta/|EQWNLVIGFL18|222|M|protein_coding|CODING|GU280_gp05|1|G);LOF=(M|GU280_gp05|1|1.00) +NC_045512.2 26635 . C T 180.0 min_af_0.050000 AF=0.001185;DP=27851;DP4=21620,6185,28,10;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A38V|222|M|protein_coding|CODING|GU280_gp05|1|T) +NC_045512.2 26763 . G A 81.0 min_af_0.050000 AF=0.000763;DP=27529;DP4=6306,21191,4,17;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A81T|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 26769 . G A 94.0 min_af_0.050000 AF=0.000832;DP=27645;DP4=6442,21176,4,19;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A83T|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 26774 . GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT G 153.0 min_af_0.050000 AF=0.000651;DP=27645;DP4=6489,21183,1,17;HRUN=2;SB=10;INDEL;EFF=FRAME_SHIFT(HIGH||gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/|ACLVGLMWLSYFIASFRLF85|222|M|protein_coding|CODING|GU280_gp05|1|G);LOF=(M|GU280_gp05|1|1.00) +NC_045512.2 26775 . GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT G 106.0 min_af_0.050000 AF=0.000508;DP=27555;DP4=6490,21192,2,12;HRUN=1;SB=2;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc|CLVGLMWLSYFIASF86F|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME) +NC_045512.2 26779 . GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT G 914.0 min_af_0.050000 AF=0.002420;DP=27690;DP4=6485,21216,9,58;HRUN=1;SB=12;INDEL;EFF=FRAME_SHIFT(HIGH||gtaggcttgatgtggctcagctacttcattgcttctttc/|VGLMWLSYFIASF88|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00) +NC_045512.2 26784 . GTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT G 242.0 min_af_0.050000 AF=0.000902;DP=27725;DP4=6544,21238,5,20;HRUN=1;SB=0;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtaggcttgatgtggctcagctacttcattgcttctttc/gtc|VGLMWLSYFIASF88V|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME) +NC_045512.2 26786 . AGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT A 574.0 min_af_0.050000 AF=0.001701;DP=27628;DP4=6442,21191,4,43;HRUN=2;SB=18;INDEL;EFF=FRAME_SHIFT(HIGH||ggcttgatgtggctcagctacttcattgcttctttc/|GLMWLSYFIASF89|222|M|protein_coding|CODING|GU280_gp05|1|A);LOF=(M|GU280_gp05|1|1.00) +NC_045512.2 26798 . G A 88.0 min_af_0.050000 AF=0.000750;DP=27989;DP4=6584,21171,7,16;SB=3;EFF=STOP_GAINED(HIGH|NONSENSE|tgG/tgA|W92*|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 26814 . G A 89.0 min_af_0.050000 AF=0.000826;DP=27845;DP4=6505,21101,5,19;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A98T|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 26839 . C T 115.0 min_af_0.050000 AF=0.001001;DP=27978;DP4=5992,21948,9,20;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T106M|222|M|protein_coding|CODING|GU280_gp05|1|T) +NC_045512.2 26887 . T C 178.0 min_af_0.050000 AF=0.000942;DP=40361;DP4=17436,22867,21,21;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V122A|222|M|protein_coding|CODING|GU280_gp05|1|C) +NC_045512.2 26889 . C T 94.0 min_af_0.050000 AF=0.000744;DP=40302;DP4=17327,22937,12,20;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P123S|222|M|protein_coding|CODING|GU280_gp05|1|T) +NC_045512.2 27076 . A G 91.0 min_af_0.050000 AF=0.001012;DP=20750;DP4=5415,15300,7,25;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q185R|222|M|protein_coding|CODING|GU280_gp05|1|G) +NC_045512.2 27131 . CTATAAAT C 85.0 min_af_0.050000 AF=0.000517;DP=21269;DP4=5687,15657,2,9;HRUN=1;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||tataaatta/|YKL204|222|M|protein_coding|CODING|GU280_gp05|1|C|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00) +NC_045512.2 27145 . C T 105.0 min_af_0.050000 AF=0.000947;DP=22170;DP4=5499,16643,8,14;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T208I|222|M|protein_coding|CODING|GU280_gp05|1|T) +NC_045512.2 27214 . G A 95.0 min_af_0.050000 AF=0.000906;DP=20964;DP4=16303,4623,16,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V5I|61|ORF6|protein_coding|CODING|GU280_gp06|1|A) +NC_045512.2 27285 . T A 122.0 min_af_0.050000 AF=0.001097;DP=20974;DP4=15962,4976,20,4;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N28K|61|ORF6|protein_coding|CODING|GU280_gp06|1|A) +NC_045512.2 27335 . C T 348.0 min_af_0.050000 AF=0.003743;DP=9350;DP4=5145,4165,25,12;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T45I|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) +NC_045512.2 27344 . A T 857.0 min_af_0.050000 AF=0.007391;DP=9336;DP4=5187,4074,34,35;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aTa|K48I|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) +NC_045512.2 27345 . A T 824.0 min_af_0.050000 AF=0.007162;DP=9355;DP4=5202,4083,34,35;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K48N|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) +NC_045512.2 27354 . A G 835.0 min_af_0.050000 AF=0.007265;DP=9085;DP4=5193,3824,37,30;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q51|61|ORF6|protein_coding|CODING|GU280_gp06|1|G) +NC_045512.2 27384 . T C 18042.0 min_af_0.050000 AF=0.039210;DP=22979;DP4=5329,16742,231,675;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C) +NC_045512.2 27476 . C T 120.0 min_af_0.050000 AF=0.001083;DP=21237;DP4=4263,16944,7,18;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T28I|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T) +NC_045512.2 27484 . T C 255.0 min_af_0.050000 AF=0.001917;DP=20866;DP4=3996,16822,10,37;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|Tta/Cta|L31|121|ORF7a|protein_coding|CODING|GU280_gp07|1|C) +NC_045512.2 27883 . C A 5191.0 PASS AF=0.163062;DP=1202;DP4=757,245,152,47;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gAc|A43D|43|ORF7b|protein_coding|CODING|GU280_gp08|1|A) +NC_045512.2 27916 . G T 383.0 min_af_0.050000 AF=0.018272;DP=1204;DP4=884,296,18,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G8V|121|ORF8|protein_coding|CODING|GU280_gp09|1|T) +NC_045512.2 28116 . G A 100.0 min_af_0.050000 AF=0.001102;DP=18155;DP4=14658,3471,15,7;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D75N|121|ORF8|protein_coding|CODING|GU280_gp09|1|A) +NC_045512.2 28121 . C T 85.0 min_af_0.050000 AF=0.000927;DP=18332;DP4=14718,3591,13,4;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I76|121|ORF8|protein_coding|CODING|GU280_gp09|1|T) +NC_045512.2 28333 . C A 188.0 min_af_0.050000 AF=0.001670;DP=19759;DP4=4578,15135,15,20;SB=20;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccC/ccA|P20|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 28346 . G T 237.0 min_af_0.050000 AF=0.001681;DP=19634;DP4=4549,15043,16,18;SB=24;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Tgc|G25C|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 28347 . G A 4058.0 min_af_0.050000 AF=0.013345;DP=19633;DP4=4498,14865,67,200;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G25D|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 28383 . CA C 138.0 min_af_0.050000 AF=0.000833;DP=19212;DP4=4193,15092,3,13;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K38|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00) +NC_045512.2 28391 . C T 95.0 min_af_0.050000 AF=0.001045;DP=19144;DP4=4089,15033,6,15;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R40C|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 28406 . TTACCCAATA T 68.0 min_af_0.050000 AF=0.000476;DP=18921;DP4=3692,15258,2,7;HRUN=3;SB=1;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttacccaataat/tat|LPNN45Y|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 28420 . T C 82.0 min_af_0.050000 AF=0.000929;DP=20450;DP4=5421,14999,5,18;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T49|419|N|protein_coding|CODING|GU280_gp10|1|C) +NC_045512.2 28727 . G A 132.0 min_af_0.050000 AF=0.001513;DP=12555;DP4=8651,3864,27,5;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A152T|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 28881 . G A 10935.0 PASS AF=0.076973;DP=6184;DP4=2898,2809,253,223;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 28882 . G A 10816.0 PASS AF=0.075656;DP=6252;DP4=2940,2836,252,223;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 28883 . G C 10619.0 PASS AF=0.075804;DP=6253;DP4=2948,2825,255,222;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C) +NC_045512.2 28987 . CCAA C 654.0 min_af_0.050000 AF=0.003439;DP=12502;DP4=2863,9632,6,37;HRUN=2;SB=6;INDEL;EFF=CODON_DELETION(MODERATE||caa/|Q242|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME) +NC_045512.2 29029 . T C 4700.0 min_af_0.050000 AF=0.011125;DP=28765;DP4=17309,11111,119,216;SB=198;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A252|419|N|protein_coding|CODING|GU280_gp10|1|C) +NC_045512.2 29031 . A G 100.0 min_af_0.050000 AF=0.000797;DP=28875;DP4=17391,11440,12,18;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E253G|419|N|protein_coding|CODING|GU280_gp10|1|G) +NC_045512.2 29039 . A T 8719.0 min_af_0.050000 AF=0.017926;DP=29232;DP4=17349,11343,226,304;SB=155;EFF=STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K256*|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29049 . G A 828.0 min_af_0.050000 AF=0.003925;DP=22418;DP4=17644,4672,80,15;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R259Q|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 29067 . CTAAAGCATACAATG C 83.0 min_af_0.050000 AF=0.000492;DP=22352;DP4=17230,5161,8,3;HRUN=1;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||aaagcatacaatgtaaca/|KAYNVT266|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00) +NC_045512.2 29187 . C T 206.0 min_af_0.050000 AF=0.002499;DP=10005;DP4=5490,4489,18,7;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A305V|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29188 . A G 173.0 min_af_0.050000 AF=0.002324;DP=9896;DP4=5450,4414,15,11;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A305|419|N|protein_coding|CODING|GU280_gp10|1|G) +NC_045512.2 29195 . GC G 256.0 min_af_0.050000 AF=0.002255;DP=9758;DP4=5491,4296,11,11;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ccc/|P309|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00) +NC_045512.2 29287 . A T 83.0 min_af_0.050000 AF=0.000864;DP=22003;DP4=4700,17278,0,19;SB=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K338N|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29511 . G T 3323.0 PASS AF=0.076433;DP=1884;DP4=1073,665,70,76;SB=28;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aTt|S413I|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29800 . G A 706.0 min_af_0.050000 AF=0.046875;DP=704;DP4=154,517,6,27;SB=1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1085841.vcf Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,229 @@ +##fileformat=VCFv4.0 +##fileDate=20201106 +##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-14951 -o /data/dnb03/galaxy_db/job_working_directory/012/246/12246264/tmp/lofreq2_call_parallelozwg3m_j/0.vcf.gz reads.bam +##reference=reference.fa +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> +##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> +##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant)."> +##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> +##FILTER=<ID=min_snvqual_77,Description="Minimum SNV Quality (Phred) 77"> +##FILTER=<ID=min_indelqual_63,Description="Minimum Indel Quality (Phred) 63"> +##FILTER=<ID=min_snvqual_81,Description="Minimum SNV Quality (Phred) 81"> +##FILTER=<ID=min_indelqual_67,Description="Minimum Indel Quality (Phred) 67"> +##FILTER=<ID=min_af_0.050000,Description="Minimum allele frequency 0.050000"> +##FILTER=<ID=min_dp_5,Description="Minimum Coverage 5"> +##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000"> +##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani" +##SnpEffCmd="SnpEff -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -stats /data/dnb03/galaxy_db/job_working_directory/012/246/12246344/outputs/galaxy_dataset_bf9af93e-df97-4905-9528-e5733fd0f335.dat NC_045512.2 /data/dnb03/galaxy_db/files/9/7/0/dataset_970a100a-939e-4af8-9511-ce9ea0a545ea.dat " +##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype [ | ERRORS | WARNINGS ] )' "> +##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +#CHROM POS ID REF ALT QUAL FILTER INFO +NC_045512.2 40 . CT C 98.0 min_af_0.050000 AF=0.003612;DP=1661;DP4=9,1646,0,6;HRUN=3;SB=0;INDEL +NC_045512.2 186 . C T 86.0 min_af_0.050000 AF=0.001217;DP=13143;DP4=8948,4173,14,5;SB=0 +NC_045512.2 241 . C T 49314.0 PASS AF=0.994071;DP=7084;DP4=0,1,3410,3672;SB=0 +NC_045512.2 323 . GT G 77.0 min_af_0.050000 AF=0.000621;DP=16109;DP4=3862,12282,3,7;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||tta/|L21|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L21|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L21|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tta/|L21|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 361 . A G 134.0 min_af_0.050000 AF=0.001169;DP=19673;DP4=7430,12213,13,12;SB=8;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G32|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G32|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G32|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G32|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G) +NC_045512.2 443 . GT G 91.0 min_af_0.050000 AF=0.001118;DP=8048;DP4=5853,2241,5,4;HRUN=4;SB=5;INDEL;EFF=FRAME_SHIFT(HIGH||ttg/|L61|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 517 . TATG T 177.0 min_af_0.050000 AF=0.002808;DP=4274;DP4=2289,2025,5,7;HRUN=1;SB=2;INDEL;EFF=CODON_DELETION(MODERATE||atg/|M85|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),CODON_DELETION(MODERATE||atg/|M85|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_DELETION(MODERATE||atg/|M85|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_DELETION(MODERATE||atg/|M85|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T) +NC_045512.2 685 . AAAGTCATTT A 94.0 min_af_0.050000 AF=0.000962;DP=9354;DP4=3244,6121,5,4;HRUN=3;SB=5;INDEL;EFF=CODON_DELETION(MODERATE||aagtcattt/|KSF141|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_DELETION(MODERATE||aagtcattt/|KSF141|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_DELETION(MODERATE||aagtcattt/|KSF141|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_DELETION(MODERATE||aagtcattt/|KSF141|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A) +NC_045512.2 1027 . T C 145.0 min_af_0.050000 AF=0.001334;DP=17235;DP4=13669,3528,24,4;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P254|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P254|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P74|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P74|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1115 . A T 221.0 min_af_0.050000 AF=0.003510;DP=6267;DP4=2472,3771,2,21;SB=26;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I284F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I284F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I104F|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I104F|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1330 . T A 202.0 min_af_0.050000 AF=0.003426;DP=5838;DP4=4195,1622,16,4;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acA|T355|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|acT/acA|T355|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|acT/acA|T175|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|acT/acA|T175|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1559 . G A 86.0 min_af_0.050000 AF=0.002454;DP=4482;DP4=1543,2924,7,6;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G432S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G432S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G252S|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G252S|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1644 . A C 264.0 min_af_0.050000 AF=0.002193;DP=14589;DP4=11414,3133,13,20;SB=58;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N460T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N460T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N280T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N280T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1647 . T A 276.0 min_af_0.050000 AF=0.002255;DP=14635;DP4=11359,3236,13,20;SB=56;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I461N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I461N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I281N|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I281N|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1656 . T A 298.0 min_af_0.050000 AF=0.002383;DP=14686;DP4=11280,3363,15,20;SB=48;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V464D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V464D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V284D|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V284D|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1659 . G T 244.0 min_af_0.050000 AF=0.002100;DP=14761;DP4=11364,3356,16,17;SB=33;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G465V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G465V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G285V|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G285V|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1702 . T C 340.0 min_af_0.050000 AF=0.002752;DP=14898;DP4=11421,3413,31,15;SB=8;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S479|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S479|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S299|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S299|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1710 . C T 138.0 min_af_0.050000 AF=0.001415;DP=14840;DP4=11402,3411,14,10;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A482V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A482V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A302V|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A302V|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1886 . G A 84.0 min_af_0.050000 AF=0.001060;DP=16031;DP4=3181,12824,3,17;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A541T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A541T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A361T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A361T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1914 . G A 136.0 min_af_0.050000 AF=0.001451;DP=14469;DP4=2859,11584,2,19;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R550H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R550H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R370H|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R370H|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1928 . G A 104.0 min_af_0.050000 AF=0.001217;DP=13965;DP4=2465,11480,5,13;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A555T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A555T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A375T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A375T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 2240 . A T 322.0 min_af_0.050000 AF=0.014104;DP=1418;DP4=289,1109,4,16;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I659F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I659F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I479F|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I479F|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 3037 . C T 49314.0 PASS AF=0.992931;DP=2122;DP4=0,1,1017,1102;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 3290 . C G 280.0 min_af_0.050000 AF=0.003124;DP=9284;DP4=7465,1786,19,10;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q1009E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q1009E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q191E|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q191E|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4054 . T C 94.0 min_af_0.050000 AF=0.002820;DP=3546;DP4=864,2667,2,9;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L1263|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L1263|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L445|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L445|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4057 . T C 103.0 min_af_0.050000 AF=0.003482;DP=3734;DP4=849,2869,1,15;SB=8;EFF=SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H1264|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H1264|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H446|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H446|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4142 . G A 107.0 min_af_0.050000 AF=0.001079;DP=18533;DP4=13023,5480,6,15;SB=40;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E1293K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E1293K|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E475K|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E475K|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4185 . G T 89.0 min_af_0.050000 AF=0.001094;DP=18280;DP4=13359,4896,11,11;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G1307V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G1307V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G489V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G489V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4216 . G A 856.0 min_af_0.050000 AF=0.007749;DP=8775;DP4=4191,4511,28,42;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L1317|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L1317|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L499|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L499|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4425 . A G 97.0 min_af_0.050000 AF=0.002182;DP=5499;DP4=2348,3137,3,9;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K1387R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K1387R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K569R|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K569R|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4428 . T C 501.0 min_af_0.050000 AF=0.007099;DP=5494;DP4=2341,3113,9,31;SB=20;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L1388S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L1388S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L570S|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L570S|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5118 . T A 201.0 min_af_0.050000 AF=0.037037;DP=270;DP4=132,128,5,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tAt|F1618Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tAt|F1618Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tAt|F800Y|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tAt|F800Y|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5119 . T A 201.0 min_af_0.050000 AF=0.036900;DP=271;DP4=133,128,5,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttA|F1618L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttA|F1618L|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttA|F800L|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttA|F800L|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5120 . T A 202.0 min_af_0.050000 AF=0.037175;DP=269;DP4=132,127,5,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y1619N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y1619N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y801N|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y801N|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5284 . C T 151.0 min_af_0.050000 AF=0.002708;DP=5908;DP4=4194,1696,5,11;SB=29;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N1673|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N1673|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N855|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N855|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5691 . C T 105.0 min_af_0.050000 AF=0.001564;DP=10869;DP4=8349,2502,13,5;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1809V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1809V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A991V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A991V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5743 . G C 536.0 min_af_0.050000;sb_fdr AF=0.007752;DP=5289;DP4=2762,2483,3,40;SB=95;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1826D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1826D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1008D|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1008D|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5744 . T C 787.0 min_af_0.050000 AF=0.010650;DP=5258;DP4=2767,2432,13,45;SB=54;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1827H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1827H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1009H|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1009H|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5765 . G A 141.0 min_af_0.050000 AF=0.003029;DP=5282;DP4=2966,2298,3,15;SB=29;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1834S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1834S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1016S|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1016S|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5805 . G A 81.0 min_af_0.050000 AF=0.001745;DP=6302;DP4=2918,3370,6,6;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C1847Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C1847Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C1029Y|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C1029Y|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5832 . C T 830.0 min_af_0.050000 AF=0.006126;DP=11754;DP4=2930,8741,13,63;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S1856F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S1856F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S1038F|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S1038F|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6173 . AT A 89.0 min_af_0.050000 AF=0.000682;DP=14653;DP4=2727,11919,2,8;HRUN=2;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||att/|I1970|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||att/|I1970|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||att/|I1152|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||att/|I1152|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 6177 . AT A 96.0 min_af_0.050000 AF=0.000678;DP=16234;DP4=2638,13599,1,10;HRUN=2;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||tat/|Y1972|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tat/|Y1972|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tat/|Y1154|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tat/|Y1154|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 6242 . C T 150.0 min_af_0.050000 AF=0.000760;DP=48682;DP4=31997,16628,29,16;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1993Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1993Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1175Y|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1175Y|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6245 . G A 107.0 min_af_0.050000 AF=0.000637;DP=48677;DP4=31963,16654,26,10;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1994I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1994I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1176I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1176I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6254 . G A 103.0 min_af_0.050000 AF=0.000673;DP=40125;DP4=32119,7966,28,5;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1997T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1997T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1179T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1179T|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6255 . C T 95.0 min_af_0.050000 AF=0.000647;DP=40215;DP4=32152,8018,23,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1997V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1997V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1179V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1179V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6271 . G A 206.0 min_af_0.050000 AF=0.001157;DP=40638;DP4=31649,8914,37,22;SB=21;EFF=SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T2002|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T2002|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1184|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1184|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6310 . C T 134.0 min_af_0.050000 AF=0.000782;DP=40919;DP4=31782,9083,30,7;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S2015|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S2015|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S1197|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S1197|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6312 . CA C 272.0 min_af_0.050000 AF=0.000811;DP=40674;DP4=31822,9010,27,6;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K2017|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K2017|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1199|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1199|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 6503 . G A 159.0 min_af_0.050000 AF=0.000902;DP=36594;DP4=6191,30357,6,32;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A2080T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A2080T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1262T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1262T|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6525 . C T 93.0 min_af_0.050000 AF=0.000746;DP=34836;DP4=4904,29889,2,27;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T2087I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T2087I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T1269I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T1269I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 7614 . G C 249.0 min_af_0.050000;sb_fdr AF=0.015337;DP=978;DP4=360,601,14,1;SB=49;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W2450S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W2450S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W1632S|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W1632S|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 7615 . G C 249.0 min_af_0.050000;sb_fdr AF=0.015306;DP=980;DP4=362,601,14,1;SB=48;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgG/tgC|W2450C|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgG/tgC|W2450C|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgG/tgC|W1632C|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgG/tgC|W1632C|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 7813 . TTC T 116.0 min_af_0.050000 AF=0.002437;DP=3283;DP4=1512,1777,6,2;HRUN=2;SB=8;INDEL;EFF=FRAME_SHIFT(HIGH||tctcat/|SH2519|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tctcat/|SH2519|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tctcat/|SH1701|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tctcat/|SH1701|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 8084 . GA G 68.0 min_af_0.050000 AF=0.001201;DP=5829;DP4=4545,1301,5,2;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K2608|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K2608|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1790|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1790|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 8927 . GT G 154.0 min_af_0.050000 AF=0.001826;DP=7669;DP4=5767,1892,6,8;HRUN=5;SB=20;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F2889|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F2889|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F126|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F126|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 8964 . CA C 94.0 min_af_0.050000 AF=0.001206;DP=7460;DP4=5950,1508,7,2;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K2901|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K2901|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K138|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K138|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 10448 . C A 49314.0 PASS AF=0.941326;DP=7465;DP4=269,49,5438,1700;SB=33;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Acc|P3395T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Acc|P3395T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Acc|P132T|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Acc|P132T|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 10527 . CT C 78.0 min_af_0.050000 AF=0.001718;DP=4074;DP4=1930,2159,3,4;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||tgt/|C3423|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C3423|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C160|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C160|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 10641 . C T 127.0 min_af_0.050000 AF=0.002277;DP=7027;DP4=2613,4397,6,10;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T3459M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T3459M|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T196M|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T196M|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 10679 . T C 886.0 min_af_0.050000 AF=0.009916;DP=6656;DP4=2234,4351,11,58;SB=29;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y3472H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y3472H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y209H|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y209H|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 10790 . C T 90.0 min_af_0.050000 AF=0.003128;DP=2877;DP4=1592,1275,6,3;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H3509Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H3509Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H246Y|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H246Y|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11071 . G GTTC 49314.0 PASS AF=0.906657;DP=17109;DP4=1189,441,11887,3625;HRUN=2;SB=29;INDEL;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTTt|F3604FF|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|GTTC|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTTt|F3604FF|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|GTTC|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTTt|F35FF|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|GTTC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTTt|F35FF|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|GTTC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME) +NC_045512.2 11074 . C CTTCT 5009.0 min_af_0.050000 AF=0.026098;DP=17511;DP4=12777,4287,354,103;HRUN=8;SB=6;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/ttCTTTt|F3604FF?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|CTTCT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTTTt|F3604FF?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|CTTCT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTTTt|F35FF?|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|CTTCT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTTTt|F35FF?|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|CTTCT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 11075 . T TTC 9644.0 min_af_0.050000 AF=0.025227;DP=17521;DP4=12767,4323,346,96;HRUN=8;SB=10;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/ttCTt|F3604F?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|TTC|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTt|F3604F?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|TTC|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTt|F35F?|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|TTC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTt|F35F?|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|TTC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 11075 . T TTCC 386.0 min_af_0.050000 AF=0.001826;DP=17521;DP4=12767,4323,24,8;HRUN=8;SB=0;INDEL;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCCTt|F3604FL|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|TTCC|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCCTt|F3604FL|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|TTCC|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCCTt|F35FL|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|TTCC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCCTt|F35FL|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|TTCC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME) +NC_045512.2 11076 . T TC 389.0 min_af_0.050000 AF=0.003118;DP=17637;DP4=13102,4493,37,18;HRUN=8;SB=6;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/ttCt|F3604F?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|TC),FRAME_SHIFT(HIGH||ttt/ttCt|F3604F?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|TC),FRAME_SHIFT(HIGH||ttt/ttCt|F35F?|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|TC|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||ttt/ttCt|F35F?|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|TC|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 11077 . T C 724.0 min_af_0.050000 AF=0.014504;DP=17650;DP4=13007,4376,127,139;SB=199;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F3604|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F3604|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F35|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F35|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11083 . G T 2124.0 min_af_0.050000 AF=0.013410;DP=17673;DP4=12902,4511,165,85;SB=23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L3606F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L3606F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L37F|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L37F|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11103 . CT C 118.0 min_af_0.050000 AF=0.000779;DP=17972;DP4=13160,4835,11,3;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F3614|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F3614|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F45|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F45|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 11750 . C T 1094.0 min_af_0.050000 AF=0.010133;DP=7895;DP4=4176,3636,40,42;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L3829F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L3829F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L260F|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L260F|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11917 . A G 90.0 min_af_0.050000 AF=0.000781;DP=25595;DP4=14208,11360,10,11;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S3884|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S3884|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S25|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S25|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12138 . C T 89.0 min_af_0.050000 AF=0.000859;DP=22110;DP4=5911,16177,6,13;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3958V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3958V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A16V|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A16V|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12152 . G A 99.0 min_af_0.050000 AF=0.000914;DP=21891;DP4=5746,16113,8,17;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3963T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3963T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A21T|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A21T|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12458 . A G 2756.0 min_af_0.050000;sb_fdr AF=0.011478;DP=15944;DP4=12445,3309,173,13;SB=65;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T4065A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T4065A|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T123A|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T123A|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12708 . C T 111.0 min_af_0.050000 AF=0.001289;DP=14745;DP4=3477,11246,5,15;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A4148V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A4148V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A8V|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A8V|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13006 . T C 101.0 min_af_0.050000 AF=0.001060;DP=17925;DP4=4485,13411,8,13;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4247|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4247|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A107|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A107|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13011 . C T 98.0 min_af_0.050000 AF=0.000962;DP=19745;DP4=4418,15301,7,13;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T4249I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T4249I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T109I|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T109I|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13034 . G A 121.0 min_af_0.050000 AF=0.000738;DP=40648;DP4=24125,16482,22,13;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4257T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4257T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13050 . C T 85.0 min_af_0.050000 AF=0.000605;DP=41322;DP4=24182,17103,17,12;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A4262V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A4262V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A9V|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A9V|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13073 . T C 82.0 min_af_0.050000 AF=0.000603;DP=41477;DP4=24012,17430,21,6;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C4270R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C4270R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C17R|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C17R|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13094 . G A 200.0 min_af_0.050000 AF=0.001158;DP=31086;DP4=23605,7439,25,14;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A4277T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A4277T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A24T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A24T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13123 . TG T 164.0 min_af_0.050000 AF=0.000748;DP=30768;DP4=22959,7835,17,6;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||gga/|G4288|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G4288|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G35|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G35|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) +NC_045512.2 13129 . A G 142.0 min_af_0.050000 AF=0.001058;DP=31184;DP4=23121,8007,32,10;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13235 . G A 137.0 min_af_0.050000 AF=0.001127;DP=28406;DP4=8123,20243,5,29;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4324T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4324T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A71T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A71T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13240 . G A 150.0 min_af_0.050000 AF=0.001122;DP=28523;DP4=8126,20358,10,25;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S4325|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S4325|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S72|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S72|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13260 . G A 143.0 min_af_0.050000 AF=0.000976;DP=31774;DP4=8264,23460,9,25;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C4332Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C4332Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C79Y|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C79Y|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13299 . TA T 128.0 min_af_0.050000 AF=0.000587;DP=30690;DP4=7825,22976,5,13;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K4346|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K4346|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K93|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K93|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) +NC_045512.2 13345 . T C 171.0 min_af_0.050000 AF=0.001096;DP=32859;DP4=10582,22225,23,18;SB=26;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4360|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4360|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P107|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P107|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13346 . G A 110.0 min_af_0.050000 AF=0.000849;DP=32974;DP4=10653,22282,18,12;SB=25;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V4361M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V4361M|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V108M|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V108M|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13350 . GT G 190.0 min_af_0.050000 AF=0.000733;DP=32739;DP4=10556,22222,8,16;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F4363|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F4363|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F110|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F110|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) +NC_045512.2 13385 . G A 159.0 min_af_0.050000 AF=0.002573;DP=10105;DP4=7996,2074,27,4;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G4374S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G4374S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G121S|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G121S|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13436 . C T 101.0 min_af_0.050000 AF=0.001858;DP=9150;DP4=6864,2269,10,7;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L4391F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L4391F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L138F|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L138F|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13541 . CT C 181.0 min_af_0.050000 AF=0.001621;DP=9872;DP4=2602,7324,2,14;HRUN=4;SB=5;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F4427|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F35|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.04) +NC_045512.2 13565 . T G 125.0 min_af_0.050000 AF=0.001695;DP=10031;DP4=2520,7488,9,8;SB=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gGa|V4434G|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gGa|V42G|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13914 . TA T 229.0 min_af_0.050000 AF=0.001064;DP=25367;DP4=5262,20193,5,22;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K4552|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K160|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 13924 . TG T 67.0 min_af_0.050000 AF=0.000391;DP=25562;DP4=4889,20711,5,5;HRUN=2;SB=15;INDEL;EFF=FRAME_SHIFT(HIGH||tgg/|W4554|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgg/|W162|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 13966 . G A 142.0 min_af_0.050000 AF=0.001330;DP=18048;DP4=14913,3101,28,2;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4568T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A176T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13982 . G A 333.0 min_af_0.050000 AF=0.002735;DP=16821;DP4=13274,3494,26,21;SB=36;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R4573H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R181H|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14061 . A G 95.0 min_af_0.050000 AF=0.001054;DP=17076;DP4=12760,4296,16,4;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L4599|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L207|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14408 . C T 49314.0 PASS AF=0.993302;DP=1941;DP4=0,0,964,976;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4715L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P323L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14581 . C T 149.0 min_af_0.050000 AF=0.001747;DP=13165;DP4=10634,2505,19,6;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H4773Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H381Y|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15324 . C T 49314.0 PASS AF=0.991877;DP=9972;DP4=5,3,7254,2709;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N5020|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N628|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15481 . T C 752.0 min_af_0.050000 AF=0.005927;DP=10967;DP4=2564,8293,51,45;SB=91;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S5073P|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S681P|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15556 . G A 135.0 min_af_0.050000 AF=0.001203;DP=22441;DP4=17610,4794,25,6;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A5098T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A706T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15682 . T A 2121.0 min_af_0.050000 AF=0.014388;DP=9730;DP4=4861,4725,78,64;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y5140N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y748N|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15685 . T A 2159.0 min_af_0.050000 AF=0.014534;DP=9770;DP4=4870,4756,79,64;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L5141M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L749M|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15723 . T C 118.0 min_af_0.050000 AF=0.001985;DP=9572;DP4=5143,4404,11,9;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D5153|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D761|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15873 . AT A 114.0 min_af_0.050000 AF=0.000652;DP=23004;DP4=18635,4358,13,2;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||tgc/|C5205|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgc/|C813|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 15878 . G A 148.0 min_af_0.050000;sb_fdr AF=0.001155;DP=23368;DP4=18628,4643,86,4;SB=43;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C5205Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C813Y|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15890 . C T 95.0 min_af_0.050000 AF=0.000866;DP=21937;DP4=16930,4986,15,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T5209I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T817I|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15962 . G A 120.0 min_af_0.050000 AF=0.001077;DP=23209;DP4=17206,5975,18,9;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G5233D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G841D|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 16073 . C T 96.0 min_af_0.050000 AF=0.000886;DP=22579;DP4=5112,17438,7,16;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A5270V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A878V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 18687 . CT C 108.0 min_af_0.050000 AF=0.000886;DP=13539;DP4=10518,3030,9,3;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||tcc/|S6143|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tcc/|S218|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 18744 . C T 102.0 min_af_0.050000 AF=0.001253;DP=13571;DP4=10434,3113,14,6;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y6160|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y235|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 18941 . A T 84.0 min_af_0.050000 AF=0.000782;DP=26854;DP4=15021,11802,3,18;SB=37;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D6226V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D301V|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 18959 . C T 144.0 min_af_0.050000 AF=0.001301;DP=18445;DP4=14957,3457,18,7;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A6232V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A307V|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 18998 . C T 103.0 min_af_0.050000 AF=0.001038;DP=18304;DP4=14106,4171,15,5;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A6245V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A320V|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19029 . C T 93.0 min_af_0.050000 AF=0.001027;DP=18494;DP4=14228,4239,16,6;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H6255|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H330|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19263 . C T 137.0 min_af_0.050000 AF=0.001291;DP=17047;DP4=2815,14204,4,21;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N6333|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N408|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19610 . C T 203.0 min_af_0.050000 AF=0.001549;DP=18718;DP4=15146,3539,29,1;SB=14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T6449I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T524I|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 19802 . G A 101.0 min_af_0.050000 AF=0.001022;DP=19577;DP4=4269,15277,7,16;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R6513H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R61H|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 20791 . G A 95.0 min_af_0.050000 AF=0.001279;DP=13295;DP4=2630,10646,5,12;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A6843T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A45T|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 20839 . G A 121.0 min_af_0.050000 AF=0.000944;DP=25429;DP4=14138,11258,14,13;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V6859I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V61I|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 20868 . TG T 93.0 min_af_0.050000 AF=0.000630;DP=17449;DP4=13993,3501,10,1;HRUN=2;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ggt/|G6869|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ggt/|G71|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.04) +NC_045512.2 20872 . G A 91.0 min_af_0.050000 AF=0.001077;DP=17635;DP4=13978,3635,14,5;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A6870T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A72T|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 20937 . G A 83.0 min_af_0.050000 AF=0.001049;DP=17166;DP4=12997,4144,14,5;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T6891|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T93|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 21054 . C T 145.0 min_af_0.050000 AF=0.001517;DP=15825;DP4=3477,12313,7,19;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y6930|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y132|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 21164 . T A 117.0 min_af_0.050000 AF=0.005592;DP=2861;DP4=2184,652,14,2;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aAa|I6967K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aAa|I169K|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 21417 . A T 140.0 min_af_0.050000 AF=0.002057;DP=8266;DP4=6203,2043,9,8;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K7051N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K253N|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 21600 . GTCAGTGTGTTAATCT G 82.0 min_af_0.050000 AF=0.000897;DP=8916;DP4=2343,6600,4,4;HRUN=1;SB=6;INDEL;EFF=CODON_DELETION(MODERATE||cagtgtgttaatctt/|QCVNL14|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME) +NC_045512.2 21634 . A AC 203.0 min_af_0.050000 AF=0.002013;DP=8943;DP4=2367,6561,6,12;HRUN=5;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||cct/ccCt|P26P?|1273|S|protein_coding|CODING|GU280_gp02|1|AC|INFO_REALIGN_3_PRIME) +NC_045512.2 21650 . A C 287.0 min_af_0.050000 AF=0.003285;DP=8827;DP4=2290,6504,4,26;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Cat|N30H|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 21656 . TTCAC T 110.0 min_af_0.050000 AF=0.001142;DP=8756;DP4=2272,6523,2,8;HRUN=3;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttcaca/|FT32|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 21714 . CT C 125.0 min_af_0.050000 AF=0.000856;DP=15185;DP4=7852,7357,12,1;HRUN=1;SB=24;INDEL;EFF=FRAME_SHIFT(HIGH||act/|T51|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 21781 . C T 708.0 min_af_0.050000 AF=0.006219;DP=9809;DP4=7177,2567,44,20;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T73|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 21875 . AT A 91.0 min_af_0.050000 AF=0.001868;DP=4283;DP4=2040,2238,3,5;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F106|1273|S|protein_coding|CODING|GU280_gp02|1|A|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 22000 . CA C 220.0 min_af_0.050000 AF=0.001903;DP=10510;DP4=4000,6529,5,15;HRUN=5;SB=5;INDEL;EFF=FRAME_SHIFT(HIGH||aac/|N148|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 22591 . C T 100.0 min_af_0.050000 AF=0.001016;DP=18694;DP4=14731,3931,20,5;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N343|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 22643 . T A 829.0 min_af_0.050000 AF=0.004008;DP=19462;DP4=14955,4414,61,17;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C361S|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 22644 . G C 795.0 min_af_0.050000 AF=0.003931;DP=19588;DP4=14973,4528,60,17;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C361S|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 22645 . T A 799.0 min_af_0.050000 AF=0.003933;DP=19578;DP4=14947,4530,66,17;SB=2;EFF=STOP_GAINED(HIGH|NONSENSE|tgT/tgA|C361*|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 22858 . C T 109.0 min_af_0.050000 AF=0.001319;DP=15163;DP4=3803,11332,6,15;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C432|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 23132 . GT G 317.0 min_af_0.050000 AF=0.003693;DP=5687;DP4=1851,3852,7,14;HRUN=3;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||tgt/|C525|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 23143 . TA T 83.0 min_af_0.050000 AF=0.001452;DP=5508;DP4=1682,3843,2,6;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K529|1273|S|protein_coding|CODING|GU280_gp02|1|T|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 23334 . CT C 89.0 min_af_0.050000 AF=0.001077;DP=8358;DP4=4251,4134,6,3;HRUN=4;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F592|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 23403 . A G 49314.0 PASS AF=0.991572;DP=17205;DP4=2,5,4395,12795;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G) +NC_045512.2 23412 . G A 108.0 min_af_0.050000 AF=0.001113;DP=17071;DP4=4291,12756,5,17;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C617Y|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 24672 . CA C 86.0 min_af_0.050000 AF=0.003731;DP=1608;DP4=428,1183,3,3;HRUN=5;SB=7;INDEL;EFF=FRAME_SHIFT(HIGH||aga/|R1039|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 24729 . C T 192.0 min_af_0.050000 AF=0.001379;DP=21760;DP4=17349,4370,24,9;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1056V|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 24770 . G A 105.0 min_af_0.050000 AF=0.000925;DP=22693;DP4=17909,4759,16,5;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1070T|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 24942 . A T 299.0 min_af_0.050000 AF=0.001816;DP=22578;DP4=5252,17272,8,35;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D1127V|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 24966 . A T 199.0 min_af_0.050000 AF=0.001429;DP=22394;DP4=5267,17072,19,16;SB=40;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aTc|N1135I|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 25047 . C T 528.0 min_af_0.050000 AF=0.002900;DP=20688;DP4=4536,16083,13,51;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P1162L|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 25607 . C T 94.0 min_af_0.050000 AF=0.001450;DP=9658;DP4=1996,7642,6,11;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A72V|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) +NC_045512.2 25646 . T G 198.0 min_af_0.050000;sb_fdr AF=0.002768;DP=9032;DP4=2052,6950,24,1;SB=140;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tGg|L85W|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) +NC_045512.2 25797 . CA C 71.0 min_af_0.050000 AF=0.003369;DP=1484;DP4=700,794,2,3;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aac/|N137|275|ORF3a|protein_coding|CODING|GU280_gp03|1|C|INFO_REALIGN_3_PRIME);LOF=(ORF3a|GU280_gp03|1|1.00) +NC_045512.2 25986 . A G 91.0 min_af_0.050000 AF=0.001282;DP=14817;DP4=11479,3318,14,6;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K198|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) +NC_045512.2 26042 . C T 987.0 min_af_0.050000 AF=0.005497;DP=15281;DP4=11400,3796,56,29;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T217I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) +NC_045512.2 26044 . C G 956.0 min_af_0.050000 AF=0.005347;DP=15148;DP4=11320,3738,53,28;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q218E|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) +NC_045512.2 26046 . A G 977.0 min_af_0.050000 AF=0.005456;DP=15213;DP4=11325,3797,56,29;SB=12;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q218|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) +NC_045512.2 26057 . A C 216.0 min_af_0.050000 AF=0.003379;DP=9469;DP4=5738,3692,20,16;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gCc|D222A|275|ORF3a|protein_coding|CODING|GU280_gp03|1|C) +NC_045512.2 26103 . T A 273.0 min_af_0.050000;sb_fdr AF=0.004015;DP=6475;DP4=3141,3308,24,2;SB=54;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V237|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) +NC_045512.2 26120 . A G 249.0 min_af_0.050000 AF=0.003769;DP=6368;DP4=3269,3073,11,13;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H243R|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) +NC_045512.2 26271 . A G 91.0 min_af_0.050000 AF=0.001094;DP=14624;DP4=3502,11102,5,11;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T9|75|E|protein_coding|CODING|GU280_gp04|1|G) +NC_045512.2 26542 . C A 757.0 min_af_0.050000 AF=0.013404;DP=3581;DP4=374,3154,5,44;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aAt|T7N|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 26545 . T G 796.0 min_af_0.050000 AF=0.003886;DP=21356;DP4=18019,3242,44,43;SB=130;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aGt|I8S|222|M|protein_coding|CODING|GU280_gp05|1|G) +NC_045512.2 26554 . A G 214.0 min_af_0.050000 AF=0.001557;DP=21840;DP4=18203,3602,20,15;SB=36;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E11G|222|M|protein_coding|CODING|GU280_gp05|1|G) +NC_045512.2 26561 . TA T 71.0 min_af_0.050000 AF=0.000541;DP=22195;DP4=18331,3864,10,2;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K15|222|M|protein_coding|CODING|GU280_gp05|1|T|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00) +NC_045512.2 26635 . C T 99.0 min_af_0.050000 AF=0.000866;DP=24240;DP4=19220,4993,16,7;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A38V|222|M|protein_coding|CODING|GU280_gp05|1|T) +NC_045512.2 26640 . G A 93.0 min_af_0.050000 AF=0.000829;DP=24139;DP4=19141,4967,15,6;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A40T|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 26695 . G C 115.0 min_af_0.050000;sb_fdr AF=0.001784;DP=8971;DP4=4073,4876,0,17;SB=41;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W58S|222|M|protein_coding|CODING|GU280_gp05|1|C) +NC_045512.2 26713 . GT G 113.0 min_af_0.050000 AF=0.001199;DP=9176;DP4=4368,4832,4,7;HRUN=4;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F65|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00) +NC_045512.2 26763 . G A 146.0 min_af_0.050000 AF=0.001152;DP=23441;DP4=5135,18267,7,21;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A81T|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 26779 . GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT G 177.0 min_af_0.050000 AF=0.000808;DP=23525;DP4=5243,18334,4,15;HRUN=1;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||gtaggcttgatgtggctcagctacttcattgcttctttc/|VGLMWLSYFIASF88|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00) +NC_045512.2 26889 . C T 117.0 min_af_0.050000 AF=0.000870;DP=34472;DP4=15378,19050,13,22;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P123S|222|M|protein_coding|CODING|GU280_gp05|1|T) +NC_045512.2 27335 . C T 287.0 min_af_0.050000 AF=0.003501;DP=8284;DP4=4742,3509,19,12;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T45I|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) +NC_045512.2 27344 . A T 384.0 min_af_0.050000 AF=0.004501;DP=8220;DP4=4741,3441,25,12;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aTa|K48I|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) +NC_045512.2 27345 . A T 406.0 min_af_0.050000 AF=0.004619;DP=8226;DP4=4747,3439,27,12;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K48N|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) +NC_045512.2 27354 . A G 302.0 min_af_0.050000 AF=0.003828;DP=7837;DP4=4560,3244,20,10;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q51|61|ORF6|protein_coding|CODING|GU280_gp06|1|G) +NC_045512.2 27377 . A G 134.0 min_af_0.050000 AF=0.001660;DP=15056;DP4=4443,10575,10,23;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E59G|61|ORF6|protein_coding|CODING|GU280_gp06|1|G) +NC_045512.2 28147 . CT C 80.0 min_af_0.050000 AF=0.000570;DP=19282;DP4=16335,2941,9,2;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F86|121|ORF8|protein_coding|CODING|GU280_gp09|1|C|INFO_REALIGN_3_PRIME);LOF=(ORF8|GU280_gp09|1|1.00) +NC_045512.2 28148 . T C 104.0 min_af_0.050000 AF=0.000984;DP=19305;DP4=16333,2941,17,2;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P85|121|ORF8|protein_coding|CODING|GU280_gp09|1|C) +NC_045512.2 28214 . CT C 129.0 min_af_0.050000 AF=0.000815;DP=20860;DP4=16749,4135,13,4;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||tta/|L109|121|ORF8|protein_coding|CODING|GU280_gp09|1|C|INFO_REALIGN_3_PRIME);LOF=(ORF8|GU280_gp09|1|1.00) +NC_045512.2 28292 . CA C 132.0 min_af_0.050000 AF=0.001453;DP=8257;DP4=4665,3660,7,5;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aat/|N8|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME) +NC_045512.2 28333 . C A 206.0 min_af_0.050000 AF=0.001636;DP=22002;DP4=4970,16986,18,21;SB=28;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccC/ccA|P20|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 28346 . G T 310.0 min_af_0.050000 AF=0.001876;DP=21859;DP4=4946,16852,23,24;SB=41;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Tgc|G25C|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 28383 . CA C 77.0 min_af_0.050000 AF=0.000532;DP=20671;DP4=4000,16733,0,11;HRUN=4;SB=8;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K38|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00) +NC_045512.2 28436 . G A 104.0 min_af_0.050000 AF=0.000961;DP=22898;DP4=6247,16623,4,20;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A55T|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 28754 . C T 81.0 min_af_0.050000 AF=0.000962;DP=16630;DP4=11578,5033,11,5;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L161F|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 28801 . C A 117.0 min_af_0.050000 AF=0.001334;DP=15738;DP4=11800,3891,9,16;SB=44;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agC/agA|S176R|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 28801 . C T 109.0 min_af_0.050000 AF=0.001271;DP=15738;DP4=11800,3891,14,8;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S176|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 28987 . CCAA C 913.0 min_af_0.050000 AF=0.003748;DP=15742;DP4=3519,12216,12,47;HRUN=2;SB=0;INDEL;EFF=CODON_DELETION(MODERATE||caa/|Q242|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME) +NC_045512.2 29029 . T C 3848.0 min_af_0.050000 AF=0.009791;DP=27984;DP4=15396,12289,102,187;SB=111;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A252|419|N|protein_coding|CODING|GU280_gp10|1|C) +NC_045512.2 29031 . A G 125.0 min_af_0.050000 AF=0.000927;DP=28044;DP4=15450,12550,11,25;SB=24;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E253G|419|N|protein_coding|CODING|GU280_gp10|1|G) +NC_045512.2 29035 . T C 147.0 min_af_0.050000 AF=0.001031;DP=28124;DP4=15520,12541,37,19;SB=9;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A254|419|N|protein_coding|CODING|GU280_gp10|1|C) +NC_045512.2 29039 . A T 8605.0 min_af_0.050000 AF=0.018320;DP=28330;DP4=15395,12395,186,341;SB=193;EFF=STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K256*|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29049 . G A 832.0 min_af_0.050000 AF=0.004347;DP=19553;DP4=15587,3863,75,15;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R259Q|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 29077 . C T 81.0 min_af_0.050000 AF=0.000856;DP=19853;DP4=15391,4437,15,4;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y268|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29127 . AT A 99.0 min_af_0.050000 AF=0.000637;DP=20411;DP4=15790,4632,10,3;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F286|419|N|protein_coding|CODING|GU280_gp10|1|A|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00) +NC_045512.2 29187 . C T 217.0 min_af_0.050000 AF=0.002703;DP=9249;DP4=5107,4112,17,11;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A305V|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29188 . A G 195.0 min_af_0.050000 AF=0.002515;DP=9144;DP4=5068,4049,15,8;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A305|419|N|protein_coding|CODING|GU280_gp10|1|G) +NC_045512.2 29195 . GC G 248.0 min_af_0.050000 AF=0.002343;DP=8962;DP4=5061,3918,12,9;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ccc/|P309|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00) +NC_045512.2 29377 . TA T 103.0 min_af_0.050000 AF=0.001989;DP=4525;DP4=3220,1474,4,5;HRUN=5;SB=8;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K370|419|N|protein_coding|CODING|GU280_gp10|1|T|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1085990.vcf Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,177 @@ +##fileformat=VCFv4.0 +##fileDate=20201106 +##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-14951 -o /data/dnb03/galaxy_db/job_working_directory/012/246/12246267/tmp/lofreq2_call_parallelqn_l60x2/0.vcf.gz reads.bam +##reference=reference.fa +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> +##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> +##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant)."> +##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> +##FILTER=<ID=min_snvqual_76,Description="Minimum SNV Quality (Phred) 76"> +##FILTER=<ID=min_indelqual_62,Description="Minimum Indel Quality (Phred) 62"> +##FILTER=<ID=min_snvqual_80,Description="Minimum SNV Quality (Phred) 80"> +##FILTER=<ID=min_indelqual_65,Description="Minimum Indel Quality (Phred) 65"> +##FILTER=<ID=min_af_0.050000,Description="Minimum allele frequency 0.050000"> +##FILTER=<ID=min_dp_5,Description="Minimum Coverage 5"> +##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000"> +##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani" +##SnpEffCmd="SnpEff -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -stats /data/dnb03/galaxy_db/job_working_directory/012/246/12246347/outputs/galaxy_dataset_1ca63e30-5487-4601-bda6-72c686cc7d32.dat NC_045512.2 /data/dnb03/galaxy_db/files/d/9/0/dataset_d9078927-a687-4f10-a32b-a57712d806a3.dat " +##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype [ | ERRORS | WARNINGS ] )' "> +##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +#CHROM POS ID REF ALT QUAL FILTER INFO +NC_045512.2 241 . C T 49314.0 PASS AF=0.994274;DP=3318;DP4=0,1,1344,1972;SB=0 +NC_045512.2 396 . A G 97.0 min_af_0.050000 AF=0.001315;DP=12924;DP4=10266,2637,16,1;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q44R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q44R|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q44R|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q44R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G) +NC_045512.2 443 . GT G 109.0 min_af_0.050000 AF=0.000905;DP=13257;DP4=10220,3055,10,2;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttg/|L61|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 527 . C T 185.0 min_af_0.050000 AF=0.003468;DP=5767;DP4=3187,2554,12,8;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L88|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L88|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L88|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L88|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T) +NC_045512.2 558 . G T 365.0 min_af_0.050000 AF=0.006082;DP=5426;DP4=3138,2252,18,16;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G98V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G98V|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G98V|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G98V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T) +NC_045512.2 656 . G T 88.0 min_af_0.050000 AF=0.001295;DP=12351;DP4=2406,9925,8,10;SB=18;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A131S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A131S|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A131S|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A131S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T) +NC_045512.2 1295 . T A 171.0 min_af_0.050000 AF=0.002789;DP=6813;DP4=1575,5217,1,18;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C344S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C344S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C164S|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C164S|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1644 . A C 184.0 min_af_0.050000 AF=0.001854;DP=12942;DP4=10851,2059,10,16;SB=67;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N460T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N460T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N280T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N280T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1647 . T A 175.0 min_af_0.050000 AF=0.001771;DP=12990;DP4=10827,2131,10,17;SB=71;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I461N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I461N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I281N|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I281N|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1656 . T A 151.0 min_af_0.050000 AF=0.001603;DP=13099;DP4=10815,2261,8,14;SB=57;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V464D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V464D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V284D|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V284D|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1659 . G T 147.0 min_af_0.050000 AF=0.001594;DP=13171;DP4=10873,2272,9,15;SB=59;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G465V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G465V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G285V|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G285V|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1702 . T C 285.0 min_af_0.050000 AF=0.002544;DP=13363;DP4=10930,2369,25,10;SB=9;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S479|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S479|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S299|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S299|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1897 . A G 87.0 min_af_0.050000 AF=0.001063;DP=15050;DP4=3734,11290,12,8;SB=30;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V544|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V544|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V364|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V364|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 1914 . G A 101.0 min_af_0.050000 AF=0.001163;DP=18060;DP4=6834,11191,7,16;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R550H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R550H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R370H|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R370H|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 2240 . A T 906.0 min_af_0.050000 AF=0.008998;DP=7335;DP4=1191,6074,1,66;SB=37;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I659F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I659F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I479F|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I479F|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 2248 . TG T 66.0 min_af_0.050000 AF=0.003336;DP=1199;DP4=1120,82,4,0;HRUN=2;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||gga/|G662|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G662|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G482|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G482|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 3037 . C T 9439.0 PASS AF=0.992278;DP=259;DP4=0,0,128,131;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 3412 . TA T 98.0 min_af_0.050000 AF=0.001304;DP=7669;DP4=1394,6276,1,9;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K1051|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K1051|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K233|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K233|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 3904 . A G 157.0 min_af_0.050000 AF=0.001423;DP=16871;DP4=13947,2891,19,6;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P1213|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P1213|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P395|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P395|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4276 . C T 89.0 min_af_0.050000 AF=0.000980;DP=17342;DP4=4361,12963,6,11;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y519|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y519|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4455 . C T 49314.0 PASS AF=0.783453;DP=4738;DP4=510,475,1930,1820;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A1397V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A1397V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A579V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A579V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5283 . A G 97.0 min_af_0.050000 AF=0.006051;DP=1322;DP4=756,557,0,9;SB=33;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1673S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1673S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N855S|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N855S|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5284 . C T 114.0 min_af_0.050000 AF=0.006798;DP=1324;DP4=754,560,1,8;SB=22;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N1673|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N1673|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N855|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N855|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5291 . CT C 137.0 min_af_0.050000 AF=0.003193;DP=2819;DP4=2233,578,5,4;HRUN=2;SB=10;INDEL;EFF=FRAME_SHIFT(HIGH||ctt/|L1676|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/|L1676|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/|L858|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/|L858|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 5365 . C T 104.0 min_af_0.050000 AF=0.003156;DP=3169;DP4=2400,758,8,3;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1700|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1700|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y882|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y882|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5629 . G A 324.0 min_af_0.050000 AF=0.007767;DP=3090;DP4=2578,487,21,4;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1788|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1788|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T970|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T970|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6173 . AT A 206.0 min_af_0.050000 AF=0.002274;DP=6597;DP4=430,6155,0,15;HRUN=2;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||att/|I1970|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||att/|I1970|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||att/|I1152|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||att/|I1152|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 6176 . GA G 85.0 min_af_0.050000 AF=0.000988;DP=8096;DP4=422,7697,0,8;HRUN=1;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||gat/|D1971|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),FRAME_SHIFT(HIGH||gat/|D1971|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),FRAME_SHIFT(HIGH||gat/|D1153|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||gat/|D1153|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 6177 . AT A 186.0 min_af_0.050000 AF=0.001680;DP=8929;DP4=413,8512,0,15;HRUN=2;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||tat/|Y1972|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tat/|Y1972|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tat/|Y1154|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tat/|Y1154|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 6242 . C T 147.0 min_af_0.050000 AF=0.000724;DP=55250;DP4=41638,13544,34,16;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1993Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1993Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1175Y|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1175Y|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6374 . G T 93.0 min_af_0.050000 AF=0.000994;DP=19124;DP4=9189,9907,9,11;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D2037Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D2037Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D1219Y|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D1219Y|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6396 . TA T 142.0 min_af_0.050000 AF=0.000800;DP=21237;DP4=9622,11810,11,6;HRUN=4;SB=8;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K2045|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K2045|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1227|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1227|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 6456 . G A 103.0 min_af_0.050000 AF=0.000659;DP=45552;DP4=8833,36673,5,30;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C2064Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C2064Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C1246Y|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C1246Y|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6503 . G A 88.0 min_af_0.050000 AF=0.000611;DP=40914;DP4=6252,34625,5,24;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A2080T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A2080T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1262T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1262T|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6513 . G T 249.0 min_af_0.050000 AF=0.001124;DP=40021;DP4=5694,34255,5,55;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aTt|S2083I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aTt|S2083I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aTt|S1265I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aTt|S1265I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 7246 . GT G 113.0 min_af_0.050000 AF=0.010067;DP=596;DP4=270,327,3,3;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttg/|L2329|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L2329|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L1511|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L1511|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 7889 . GT G 115.0 min_af_0.050000 AF=0.001985;DP=5039;DP4=1008,4028,3,7;HRUN=5;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F2543|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F2543|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F1725|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F1725|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 9656 . A G 748.0 min_af_0.050000;sb_fdr AF=0.010109;DP=5243;DP4=2338,2850,51,3;SB=137;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M3131V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M3131V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M368V|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M368V|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 9811 . CT C 124.0 min_af_0.050000 AF=0.001097;DP=12759;DP4=1985,10818,1,13;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttg/|L3184|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L3184|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L421|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L421|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 10409 . A G 102.0 min_af_0.050000 AF=0.002045;DP=5868;DP4=2189,3666,5,7;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N3382D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N3382D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N119D|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N119D|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 10511 . G A 49314.0 PASS AF=0.781399;DP=2301;DP4=353,134,1375,438;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D3416N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D3416N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D153N|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D153N|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 10783 . AC A 1328.0 min_af_0.050000 AF=0.030864;DP=1782;DP4=775,955,10,45;HRUN=1;SB=41;INDEL;EFF=FRAME_SHIFT(HIGH||caa/|Q3507|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),FRAME_SHIFT(HIGH||caa/|Q3507|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),FRAME_SHIFT(HIGH||caa/|Q244|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||caa/|Q244|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 10986 . G T 245.0 min_af_0.050000 AF=0.004993;DP=4206;DP4=1217,2968,7,14;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aTa|R3574I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aTa|R3574I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aTa|R5I|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aTa|R5I|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11003 . C T 136.0 min_af_0.050000 AF=0.003531;DP=4531;DP4=1176,3339,6,10;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H3580Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H3580Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H11Y|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H11Y|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11071 . G GTTC 49314.0 PASS AF=0.921222;DP=13811;DP4=910,220,10234,2489;HRUN=2;SB=0;INDEL;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTTt|F3604FF|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|GTTC|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTTt|F3604FF|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|GTTC|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTTt|F35FF|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|GTTC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTTt|F35FF|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|GTTC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME) +NC_045512.2 11074 . C CTTCT 3604.0 min_af_0.050000 AF=0.024274;DP=14007;DP4=10839,2872,285,55;HRUN=8;SB=14;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/ttCTTTt|F3604FF?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|CTTCT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTTTt|F3604FF?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|CTTCT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTTTt|F35FF?|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|CTTCT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTTTt|F35FF?|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|CTTCT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 11075 . T TTC 6655.0 min_af_0.050000 AF=0.021513;DP=14038;DP4=10846,2884,246,56;HRUN=8;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/ttCTt|F3604F?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|TTC|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTt|F3604F?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|TTC|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTt|F35F?|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|TTC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTt|F35F?|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|TTC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 11075 . T TTCC 117.0 min_af_0.050000 AF=0.000855;DP=14038;DP4=10846,2884,11,1;HRUN=8;SB=3;INDEL;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCCTt|F3604FL|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|TTCC|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCCTt|F3604FL|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|TTCC|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCCTt|F35FL|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|TTCC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCCTt|F35FL|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|TTCC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME) +NC_045512.2 11076 . T TC 116.0 min_af_0.050000 AF=0.001273;DP=14138;DP4=11112,3018,6,12;HRUN=8;SB=43;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/ttCt|F3604F?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|TC),FRAME_SHIFT(HIGH||ttt/ttCt|F3604F?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|TC),FRAME_SHIFT(HIGH||ttt/ttCt|F35F?|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|TC|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||ttt/ttCt|F35F?|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|TC|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 11077 . T C 300.0 min_af_0.050000 AF=0.008197;DP=14151;DP4=11058,2972,63,56;SB=92;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F3604|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F3604|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F35|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F35|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11083 . G T 436.0 min_af_0.050000 AF=0.005129;DP=14232;DP4=11065,3081,62,22;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L3606F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L3606F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L37F|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L37F|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 11983 . A T 101.0 min_af_0.050000 AF=0.001169;DP=15398;DP4=12255,3117,13,6;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaT|E3906D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaT|E3906D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaT|E47D|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaT|E47D|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12164 . G T 645.0 min_af_0.050000 AF=0.003440;DP=18898;DP4=5086,13740,17,49;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A3967S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A3967S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A25S|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A25S|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12458 . A G 22986.0 PASS AF=0.118809;DP=7693;DP4=4150,2622,687,233;SB=151;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T4065A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T4065A|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T123A|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T123A|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12831 . A G 88.0 min_af_0.050000 AF=0.000898;DP=20042;DP4=16187,3831,14,5;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q4189R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q4189R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q49R|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q49R|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13006 . T C 128.0 min_af_0.050000 AF=0.001106;DP=22613;DP4=4970,17609,8,18;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4247|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4247|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A107|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A107|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13011 . C T 86.0 min_af_0.050000 AF=0.000804;DP=26106;DP4=4889,21186,8,14;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T4249I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T4249I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T109I|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T109I|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13034 . G A 95.0 min_af_0.050000 AF=0.000506;DP=69235;DP4=45709,23472,20,21;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4257T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4257T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13048 . T C 181.0 min_af_0.050000 AF=0.000682;DP=70402;DP4=45971,24198,44,166;SB=390;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4261|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4261|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P8|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P8|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13049 . G A 164.0 min_af_0.050000 AF=0.000651;DP=70714;DP4=46084,24548,36,18;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4262T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4262T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A9T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A9T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13073 . T C 106.0 min_af_0.050000 AF=0.000530;DP=71755;DP4=46248,25458,25,18;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C4270R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C4270R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C17R|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C17R|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13094 . G A 110.0 min_af_0.050000 AF=0.000604;DP=57907;DP4=46186,11671,29,10;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A4277T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A4277T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A24T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A24T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13123 . TG T 362.0 min_af_0.050000 AF=0.000845;DP=57968;DP4=45262,12745,39,10;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||gga/|G4288|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G4288|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G35|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G35|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) +NC_045512.2 13129 . A G 275.0 min_af_0.050000 AF=0.001106;DP=58773;DP4=45596,13058,79,15;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13235 . G A 225.0 min_af_0.050000 AF=0.001046;DP=58324;DP4=13189,45056,12,53;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4324T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4324T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A71T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A71T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13240 . G A 168.0 min_af_0.050000 AF=0.000823;DP=58314;DP4=13132,45114,15,36;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S4325|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S4325|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S72|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S72|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13260 . G A 201.0 min_af_0.050000 AF=0.000834;DP=59945;DP4=13428,46442,16,42;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C4332Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C4332Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C79Y|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C79Y|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13288 . AT A 246.0 min_af_0.050000 AF=0.000600;DP=58346;DP4=12587,45733,5,30;HRUN=4;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||tgt/|C4343|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C4343|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C90|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C90|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) +NC_045512.2 13345 . T C 83.0 min_af_0.050000 AF=0.000573;DP=55875;DP4=12086,43726,9,28;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4360|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4360|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P107|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P107|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13350 . GT G 253.0 min_af_0.050000 AF=0.000632;DP=55344;DP4=11847,43567,6,29;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F4363|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F4363|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F110|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F110|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11) +NC_045512.2 13565 . T G 345.0 min_af_0.050000 AF=0.004812;DP=6235;DP4=1296,4904,18,12;SB=54;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gGa|V4434G|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gGa|V42G|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13571 . G T 479.0 min_af_0.050000 AF=0.006221;DP=6269;DP4=1318,4908,5,37;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G4436V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G44V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13650 . T G 148.0 min_af_0.050000;sb_fdr AF=0.000779;DP=43663;DP4=33531,10080,3,32;SB=168;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttG|F4462L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttG|F70L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14267 . C T 87.0 min_af_0.050000 AF=0.001143;DP=13128;DP4=8606,4502,9,7;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T4668M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T276M|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14408 . C T 49314.0 PASS AF=0.993192;DP=3966;DP4=0,0,1935,2031;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4715L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P323L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15324 . C T 49314.0 PASS AF=0.988437;DP=11935;DP4=1,2,9099,2830;SB=8;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N5020|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N628|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15481 . T C 328.0 min_af_0.050000 AF=0.002827;DP=13441;DP4=2511,10857,40,27;SB=127;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S5073P|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S681P|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15568 . A C 180.0 min_af_0.050000 AF=0.002297;DP=10448;DP4=8328,2090,17,9;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Cct|T5102P|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Cct|T710P|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15673 . T G 106.0 min_af_0.050000;sb_fdr AF=0.004279;DP=4674;DP4=2599,2037,25,1;SB=50;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Gtt|F5137V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Gtt|F745V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15682 . T A 1300.0 min_af_0.050000 AF=0.017751;DP=4563;DP4=2587,1892,47,35;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y5140N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y748N|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15685 . T A 1323.0 min_af_0.050000 AF=0.017982;DP=4560;DP4=2573,1902,46,36;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L5141M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L749M|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 16026 . A T 151.0 min_af_0.050000 AF=0.004022;DP=3481;DP4=1737,1726,1,15;SB=32;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttA/ttT|L5254F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttA/ttT|L862F|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 16030 . A G 152.0 min_af_0.050000;sb_fdr AF=0.004060;DP=3448;DP4=1751,1682,0,14;SB=43;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5256V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I864V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 17122 . G A 82.0 min_af_0.050000 AF=0.001070;DP=14013;DP4=7804,6183,14,7;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A5620T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A296T|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 17146 . A G 85.0 min_af_0.050000 AF=0.001464;DP=9561;DP4=7533,1983,9,5;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5628V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I304V|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 18687 . CT C 132.0 min_af_0.050000 AF=0.000757;DP=21142;DP4=16971,4200,11,5;HRUN=4;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||tcc/|S6143|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tcc/|S218|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 18859 . G A 80.0 min_af_0.050000 AF=0.000826;DP=20592;DP4=4201,16371,5,12;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A6199T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A274T|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 18941 . A T 392.0 min_af_0.050000 AF=0.002016;DP=24798;DP4=8527,16211,9,44;SB=20;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D6226V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D301V|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 22000 . CA C 81.0 min_af_0.050000 AF=0.001893;DP=3697;DP4=1829,1873,5,2;HRUN=5;SB=5;INDEL;EFF=FRAME_SHIFT(HIGH||aac/|N148|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 22091 . A G 359.0 min_af_0.050000 AF=0.010671;DP=2249;DP4=1794,428,21,3;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M177V|1273|S|protein_coding|CODING|GU280_gp02|1|G) +NC_045512.2 22643 . T A 168.0 min_af_0.050000 AF=0.003589;DP=4458;DP4=3614,824,12,4;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C361S|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 22644 . G C 129.0 min_af_0.050000 AF=0.003124;DP=4481;DP4=3615,850,11,3;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C361S|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 22645 . T A 151.0 min_af_0.050000 AF=0.003350;DP=4478;DP4=3605,849,14,3;SB=0;EFF=STOP_GAINED(HIGH|NONSENSE|tgT/tgA|C361*|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 22805 . AC A 70.0 min_af_0.050000 AF=0.001232;DP=4871;DP4=723,4147,0,6;HRUN=1;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||act/|T415|1273|S|protein_coding|CODING|GU280_gp02|1|A);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 22899 . G T 250.0 min_af_0.050000 AF=0.002593;DP=12339;DP4=9701,2594,28,9;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G446V|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 23131 . TG T 97.0 min_af_0.050000 AF=0.000820;DP=12195;DP4=2479,9746,1,9;HRUN=1;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||gtt/|V524|1273|S|protein_coding|CODING|GU280_gp02|1|T);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 23143 . TA T 127.0 min_af_0.050000 AF=0.001144;DP=12243;DP4=2290,9978,0,14;HRUN=5;SB=10;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K529|1273|S|protein_coding|CODING|GU280_gp02|1|T|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 23205 . G A 87.0 min_af_0.050000 AF=0.000720;DP=30549;DP4=19078,11434,15,7;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G548D|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 23238 . T C 182.0 min_af_0.050000 AF=0.001117;DP=31346;DP4=19348,11952,9,31;SB=62;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tCt|F559S|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 23261 . A G 132.0 min_af_0.050000 AF=0.001092;DP=26563;DP4=18642,7879,25,8;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R567G|1273|S|protein_coding|CODING|GU280_gp02|1|G) +NC_045512.2 23302 . G A 137.0 min_af_0.050000 AF=0.001764;DP=10768;DP4=5127,5611,17,4;SB=24;EFF=SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q580|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 23306 . C G 116.0 min_af_0.050000 AF=0.001570;DP=10826;DP4=5174,5631,14,3;SB=22;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Gtt|L582V|1273|S|protein_coding|CODING|GU280_gp02|1|G) +NC_045512.2 23403 . A G 49314.0 PASS AF=0.991045;DP=24567;DP4=3,5,5490,19063;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G) +NC_045512.2 23417 . G T 465.0 min_af_0.050000 AF=0.002290;DP=24458;DP4=5401,18993,18,40;SB=9;EFF=STOP_GAINED(HIGH|NONSENSE|Gaa/Taa|E619*|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 24729 . C T 88.0 min_af_0.050000 AF=0.001045;DP=15304;DP4=11983,3304,14,2;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1056V|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 24776 . GA G 68.0 min_af_0.050000 AF=0.000587;DP=15338;DP4=12278,3058,6,3;HRUN=4;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K1073|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 24883 . G A 138.0 min_af_0.050000 AF=0.002752;DP=5813;DP4=2679,3117,8,8;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R1107|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 24933 . G T 358.0 min_af_0.050000 AF=0.002817;DP=14552;DP4=2925,11563,9,51;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G1124V|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 24942 . A T 251.0 min_af_0.050000 AF=0.002129;DP=14564;DP4=2931,11594,5,30;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D1127V|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 25132 . C A 105.0 min_af_0.050000 AF=0.009537;DP=734;DP4=504,222,5,3;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A1190|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512.2 25379 . A T 122.0 min_af_0.050000 AF=0.001291;DP=16270;DP4=13436,2805,11,10;SB=28;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Tca|T1273S|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 25543 . G A 86.0 min_af_0.050000 AF=0.000993;DP=17112;DP4=3351,13735,4,14;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A51T|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) +NC_045512.2 25635 . C T 81.0 min_af_0.050000 AF=0.000911;DP=17568;DP4=4208,13332,5,15;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C81|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) +NC_045512.2 25646 . T G 149.0 min_af_0.050000;sb_fdr AF=0.001557;DP=17345;DP4=4081,13232,23,4;SB=106;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tGg|L85W|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) +NC_045512.2 25797 . CA C 136.0 min_af_0.050000 AF=0.004646;DP=1937;DP4=832,1134,5,4;HRUN=5;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||aac/|N137|275|ORF3a|protein_coding|CODING|GU280_gp03|1|C|INFO_REALIGN_3_PRIME);LOF=(ORF3a|GU280_gp03|1|1.00) +NC_045512.2 26042 . C T 456.0 min_af_0.050000 AF=0.003753;DP=11725;DP4=8878,2799,31,15;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T217I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) +NC_045512.2 26044 . C G 445.0 min_af_0.050000 AF=0.003696;DP=11634;DP4=8840,2742,30,14;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q218E|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) +NC_045512.2 26046 . A G 446.0 min_af_0.050000 AF=0.003765;DP=11688;DP4=8854,2787,32,14;SB=5;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q218|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G) +NC_045512.2 26089 . T A 116.0 min_af_0.050000 AF=0.002761;DP=4709;DP4=2229,2464,3,12;SB=14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Aac|Y233N|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) +NC_045512.2 26103 . T A 159.0 min_af_0.050000 AF=0.003338;DP=4793;DP4=2379,2397,14,2;SB=26;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V237|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A) +NC_045512.2 26270 . C T 88.0 min_af_0.050000 AF=0.001211;DP=11557;DP4=2704,8836,4,10;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T) +NC_045512.2 26542 . C A 168.0 min_af_0.050000 AF=0.004989;DP=2806;DP4=185,2601,1,13;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aAt|T7N|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 26545 . T G 786.0 min_af_0.050000 AF=0.004062;DP=19450;DP4=16700,2664,68,12;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aGt|I8S|222|M|protein_coding|CODING|GU280_gp05|1|G) +NC_045512.2 26554 . A G 217.0 min_af_0.050000 AF=0.001613;DP=19843;DP4=16861,2946,28,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E11G|222|M|protein_coding|CODING|GU280_gp05|1|G) +NC_045512.2 26635 . C T 83.0 min_af_0.050000 AF=0.000830;DP=21692;DP4=17729,3934,19,3;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A38V|222|M|protein_coding|CODING|GU280_gp05|1|T) +NC_045512.2 26695 . G C 144.0 min_af_0.050000;sb_fdr AF=0.002401;DP=7079;DP4=3264,3797,0,17;SB=45;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W58S|222|M|protein_coding|CODING|GU280_gp05|1|C) +NC_045512.2 26713 . GT G 108.0 min_af_0.050000 AF=0.001325;DP=7547;DP4=3518,4048,3,7;HRUN=4;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F65|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00) +NC_045512.2 26889 . C T 105.0 min_af_0.050000 AF=0.000846;DP=36631;DP4=17521,19069,15,18;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P123S|222|M|protein_coding|CODING|GU280_gp05|1|T) +NC_045512.2 26895 . C T 124.0 min_af_0.050000 AF=0.001078;DP=20410;DP4=17437,2947,21,3;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H125Y|222|M|protein_coding|CODING|GU280_gp05|1|T) +NC_045512.2 27059 . C T 383.0 min_af_0.050000 AF=0.003588;DP=11426;DP4=4376,7002,17,25;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y179|222|M|protein_coding|CODING|GU280_gp05|1|T) +NC_045512.2 27079 . G A 86.0 min_af_0.050000 AF=0.000875;DP=21704;DP4=4481,17197,2,17;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R186H|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 27105 . G A 117.0 min_af_0.050000 AF=0.001008;DP=21817;DP4=4582,17206,6,16;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A195T|222|M|protein_coding|CODING|GU280_gp05|1|A) +NC_045512.2 27120 . A G 85.0 min_af_0.050000 AF=0.000830;DP=21676;DP4=4482,17172,4,14;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Ggg|R200G|222|M|protein_coding|CODING|GU280_gp05|1|G) +NC_045512.2 27214 . G A 86.0 min_af_0.050000 AF=0.001126;DP=13325;DP4=11074,2235,9,6;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V5I|61|ORF6|protein_coding|CODING|GU280_gp06|1|A) +NC_045512.2 27335 . C T 214.0 min_af_0.050000 AF=0.004064;DP=4921;DP4=2786,2115,15,5;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T45I|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) +NC_045512.2 27344 . A T 333.0 min_af_0.050000 AF=0.005777;DP=4847;DP4=2763,2055,20,8;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aTa|K48I|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) +NC_045512.2 27345 . A T 322.0 min_af_0.050000 AF=0.005784;DP=4841;DP4=2760,2050,20,8;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K48N|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) +NC_045512.2 27354 . A G 354.0 min_af_0.050000 AF=0.006365;DP=4556;DP4=2590,1937,21,8;SB=8;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q51|61|ORF6|protein_coding|CODING|GU280_gp06|1|G) +NC_045512.2 28333 . C A 829.0 min_af_0.050000 AF=0.006612;DP=13007;DP4=2288,10630,42,45;SB=100;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccC/ccA|P20|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 28346 . G T 1405.0 min_af_0.050000 AF=0.008030;DP=12951;DP4=2278,10563,52,53;SB=128;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Tgc|G25C|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 28849 . C T 253.0 min_af_0.050000 AF=0.008879;DP=2140;DP4=1054,1067,9,10;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N192|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29029 . T C 2047.0 min_af_0.050000 AF=0.004975;DP=36379;DP4=28535,7633,126,74;SB=64;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A252|419|N|protein_coding|CODING|GU280_gp10|1|C) +NC_045512.2 29039 . A T 5675.0 min_af_0.050000 AF=0.010564;DP=37106;DP4=28670,8011,189,214;SB=413;EFF=STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K256*|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29044 . G A 616.0 min_af_0.050000 AF=0.002272;DP=34327;DP4=28857,5335,105,15;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K257|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 29049 . G A 646.0 min_af_0.050000 AF=0.002444;DP=34783;DP4=28968,5690,85,10;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R259Q|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 29186 . G A 114.0 min_af_0.050000 AF=0.001532;DP=12404;DP4=6845,5536,15,6;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A305T|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 29187 . C T 142.0 min_af_0.050000 AF=0.001691;DP=12417;DP4=6915,5477,13,9;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A305V|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29188 . A G 134.0 min_af_0.050000 AF=0.001629;DP=12279;DP4=6876,5376,13,11;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A305|419|N|protein_coding|CODING|GU280_gp10|1|G) +NC_045512.2 29195 . GC G 297.0 min_af_0.050000 AF=0.002159;DP=12041;DP4=6921,5152,14,12;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ccc/|P309|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00) +NC_045512.2 29235 . G A 83.0 min_af_0.050000 AF=0.000626;DP=36745;DP4=6926,29793,7,17;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G321D|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 29312 . A G 145.0 min_af_0.050000 AF=0.000883;DP=33979;DP4=4770,29170,1,30;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Gaa|K347E|419|N|protein_coding|CODING|GU280_gp10|1|G) +NC_045512.2 29320 . A G 106.0 min_af_0.050000 AF=0.000762;DP=34141;DP4=5096,29012,4,26;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q349|419|N|protein_coding|CODING|GU280_gp10|1|G) +NC_045512.2 29331 . T C 99.0 min_af_0.050000 AF=0.000719;DP=33388;DP4=4576,28723,2,67;SB=23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L353P|419|N|protein_coding|CODING|GU280_gp10|1|C)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input436.tabular Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,12 @@ +CHROM POS REF ALT AF EFF[*].AA EFF[*].GENE EFF[*].EFFECT +NC_045512 241 C T 0.992195 +NC_045512 685 AAAGTCATTT A 0.363753 KSF141 ORF1ab CODON_DELETION +NC_045512 1059 C T 0.988211 T265I ORF1ab NON_SYNONYMOUS_CODING +NC_045512 3037 C T 0.988485 F924 ORF1ab SYNONYMOUS_CODING +NC_045512 9479 G T 0.991964 G3072C ORF1ab NON_SYNONYMOUS_CODING +NC_045512 14408 C T 0.983607 P4720L ORF1ab NON_SYNONYMOUS_CODING +NC_045512 21204 G T 0.982705 K6985N ORF1ab NON_SYNONYMOUS_CODING +NC_045512 23403 A G 0.986115 D614G S NON_SYNONYMOUS_CODING +NC_045512 23582 TATCAGACTCAGACTA T 0.272585 QTQTN675 S CODON_DELETION +NC_045512 25563 G T 0.990244 Q57H ORF3a NON_SYNONYMOUS_CODING +NC_045512 29511 G T 0.990254 S413I N NON_SYNONYMOUS_CODING
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input437.tabular Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,13 @@ +CHROM POS REF ALT AF EFF[*].AA EFF[*].GENE EFF[*].EFFECT +NC_045512 241 C T 0.983181 +NC_045512 3037 C T 0.981162 F924 ORF1ab SYNONYMOUS_CODING +NC_045512 11077 T C 0.970068 F3604 ORF1ab SYNONYMOUS_CODING +NC_045512 13059 C T 0.983112 T4265I ORF1ab NON_SYNONYMOUS_CODING +NC_045512 14408 C T 0.982935 P4720L ORF1ab NON_SYNONYMOUS_CODING +NC_045512 15324 C T 0.982808 N5025 ORF1ab SYNONYMOUS_CODING +NC_045512 16949 C T 0.987941 P5567L ORF1ab NON_SYNONYMOUS_CODING +NC_045512 21974 G T 0.32243 D138Y S NON_SYNONYMOUS_CODING +NC_045512 23403 A G 0.977044 D614G S NON_SYNONYMOUS_CODING +NC_045512 26822 C T 0.377177 F100 M SYNONYMOUS_CODING +NC_045512 27503 C T 0.308917 S37F ORF7a NON_SYNONYMOUS_CODING +NC_045512 27720 TATA T 0.975973 IT110T ORF7a CODON_CHANGE_PLUS_CODON_DELETION
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input438.tabular Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,8 @@ +CHROM POS REF ALT AF EFF[*].AA EFF[*].GENE EFF[*].EFFECT +NC_045512 241 C T 0.973039 +NC_045512 3037 C T 0.991736 F924 ORF1ab SYNONYMOUS_CODING +NC_045512 11077 T C 0.992647 F3604 ORF1ab SYNONYMOUS_CODING +NC_045512 14408 C T 0.976879 P4720L ORF1ab NON_SYNONYMOUS_CODING +NC_045512 15324 C T 0.988281 N5025 ORF1ab SYNONYMOUS_CODING +NC_045512 22206 A G 0.316176 D215G S NON_SYNONYMOUS_CODING +NC_045512 23403 A G 0.98503 D614G S NON_SYNONYMOUS_CODING
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input439.tabular Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,15 @@ +CHROM POS REF ALT AF EFF[*].AA EFF[*].GENE EFF[*].EFFECT +NC_045512 241 C T 0.983923 +NC_045512 1059 C T 0.8606959999999999 T265I ORF1ab NON_SYNONYMOUS_CODING +NC_045512 3037 C T 0.983871 F924 ORF1ab SYNONYMOUS_CODING +NC_045512 3373 C A 0.166667 D1036E ORF1ab NON_SYNONYMOUS_CODING +NC_045512 14408 C T 0.995049 P4720L ORF1ab NON_SYNONYMOUS_CODING +NC_045512 15689 G A 0.344322 R5147H ORF1ab NON_SYNONYMOUS_CODING +NC_045512 23403 A G 0.94386 D614G S NON_SYNONYMOUS_CODING +NC_045512 25563 G T 0.751445 Q57H ORF3a NON_SYNONYMOUS_CODING +NC_045512 26259 TTCGGAAGAGACAGGTACGTTAATA T 0.183168 SEETGTLI6 E CODON_DELETION +NC_045512 27883 C A 0.5544789999999999 A43D ORF7b NON_SYNONYMOUS_CODING +NC_045512 27916 G T 0.139037 G8V ORF8 NON_SYNONYMOUS_CODING +NC_045512 28881 G A 0.108696 R203K N NON_SYNONYMOUS_CODING +NC_045512 28882 G A 0.104859 R203 N SYNONYMOUS_CODING +NC_045512 28883 G C 0.107417 G204R N NON_SYNONYMOUS_CODING
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input440.tabular Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,10 @@ +CHROM POS REF ALT AF EFF[*].AA EFF[*].GENE EFF[*].EFFECT +NC_045512 241 C T 0.982353 +NC_045512 3037 C T 0.985075 F924 ORF1ab SYNONYMOUS_CODING +NC_045512 10776 C T 0.68 P3504L ORF1ab NON_SYNONYMOUS_CODING +NC_045512 11071 G GTTC 0.841463 F3604FF ORF1ab CODON_CHANGE_PLUS_CODON_INSERTION +NC_045512 11083 G T 0.163636 L3606F ORF1ab NON_SYNONYMOUS_CODING +NC_045512 13131 A G 0.250464 Q4289R ORF1ab NON_SYNONYMOUS_CODING +NC_045512 14408 C T 0.986072 P4720L ORF1ab NON_SYNONYMOUS_CODING +NC_045512 15324 C T 0.988713 N5025 ORF1ab SYNONYMOUS_CODING +NC_045512 23403 A G 0.988673 D614G S NON_SYNONYMOUS_CODING
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input441.tabular Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,9 @@ +CHROM POS REF ALT AF EFF[*].AA EFF[*].GENE EFF[*].EFFECT +NC_045512 241 C T 0.980716 +NC_045512 424 AGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTT A 0.565371 VEVEKGVLPQLE54E ORF1ab CODON_CHANGE_PLUS_CODON_DELETION +NC_045512 457 T TA 0.11413 E65R? ORF1ab FRAME_SHIFT +NC_045512 3037 C T 0.96063 F924 ORF1ab SYNONYMOUS_CODING +NC_045512 6906 C T 0.988571 S2214L ORF1ab NON_SYNONYMOUS_CODING +NC_045512 14408 C T 0.962366 P4720L ORF1ab NON_SYNONYMOUS_CODING +NC_045512 15324 C T 0.992674 N5025 ORF1ab SYNONYMOUS_CODING +NC_045512 23403 A G 0.969309 D614G S NON_SYNONYMOUS_CODING
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input442.tabular Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,8 @@ +CHROM POS REF ALT AF EFF[*].AA EFF[*].GENE EFF[*].EFFECT +NC_045512 241 C T 0.97907 +NC_045512 3037 C T 0.952381 F924 ORF1ab SYNONYMOUS_CODING +NC_045512 11071 G GTTC 0.112 F3604FF ORF1ab CODON_CHANGE_PLUS_CODON_INSERTION +NC_045512 11077 T C 0.857143 F3604 ORF1ab SYNONYMOUS_CODING +NC_045512 14408 C T 0.975904 P4720L ORF1ab NON_SYNONYMOUS_CODING +NC_045512 15324 C T 0.992806 N5025 ORF1ab SYNONYMOUS_CODING +NC_045512 23403 A G 0.982808 D614G S NON_SYNONYMOUS_CODING
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input443.tabular Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,9 @@ +CHROM POS REF ALT AF EFF[*].AA EFF[*].GENE EFF[*].EFFECT +NC_045512 21 C T 0.980392 +NC_045512 241 C T 0.981265 +NC_045512 3037 C T 0.983333 F924 ORF1ab SYNONYMOUS_CODING +NC_045512 14408 C T 0.985 P4720L ORF1ab NON_SYNONYMOUS_CODING +NC_045512 14520 C T 0.987179 N4757 ORF1ab SYNONYMOUS_CODING +NC_045512 15324 C T 0.972332 N5025 ORF1ab SYNONYMOUS_CODING +NC_045512 23403 A G 0.97929 D614G S NON_SYNONYMOUS_CODING +NC_045512 26354 T G 0.309524 L37R E NON_SYNONYMOUS_CODING
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input444.tabular Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,7 @@ +CHROM POS REF ALT AF EFF[*].AA EFF[*].GENE EFF[*].EFFECT +NC_045512 241 C T 1.0 +NC_045512 3037 C T 0.984375 F924 ORF1ab SYNONYMOUS_CODING +NC_045512 17999 C T 0.10352 T5917I ORF1ab NON_SYNONYMOUS_CODING +NC_045512 23403 A G 0.982533 D614G S NON_SYNONYMOUS_CODING +NC_045512 26256 CGTTTCGGAAGAGACAGGTACGTTAATA C 0.154639 SEETGTLIV6 E CODON_DELETION +NC_045512 26259 TTCGGAAGAGACAGGTACGTTAATA T 0.511278 SEETGTLI6 E CODON_DELETION
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snpeff.123.vcf Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,51 @@ +##fileformat=VCFv4.0 +##fileDate=20200707 +##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-14951 -o /data/dnb02/galaxy_db/job_working_directory/009/430/9430166/working/pp-tmp/lofreq2_call_parallelpfou9vt9/0.vcf.gz reads.bam +##reference=reference.fa +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> +##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> +##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant)."> +##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> +##FILTER=<ID=min_snvqual_66,Description="Minimum SNV Quality (Phred) 66"> +##FILTER=<ID=min_indelqual_52,Description="Minimum Indel Quality (Phred) 52"> +##FILTER=<ID=min_snvqual_70,Description="Minimum SNV Quality (Phred) 70"> +##FILTER=<ID=min_indelqual_57,Description="Minimum Indel Quality (Phred) 57"> +##FILTER=<ID=min_af_0.050000,Description="Minimum allele frequency 0.050000"> +##FILTER=<ID=min_dp_5,Description="Minimum Coverage 5"> +##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000"> +##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani" +##SnpEffCmd="SnpEff -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -no-utr -stats /data/dnb02/galaxy_db/job_working_directory/009/430/9430172/galaxy_dataset_24243789.dat NC_045512.2 /data/dnb02/galaxy_db/files/022/094/dataset_22094491.dat " +##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype [ | ERRORS | WARNINGS ] )' "> +##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +#CHROM POS ID REF ALT QUAL FILTER INFO +NC_045512.2 241 . C T 13172.0 PASS DP=363;AF=0.980716;SB=0;DP4=1,1,167,193 +NC_045512.2 424 . AGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTT A 6194.0 PASS DP=283;AF=0.565371;SB=0;DP4=76,47,98,62;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtagaagttgaaaaaggcgttttgcctcaacttgaa/gaa|VEVEKGVLPQLE54E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtagaagttgaaaaaggcgttttgcctcaacttgaa/gaa|VEVEKGVLPQLE54E|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtagaagttgaaaaaggcgttttgcctcaacttgaa/gaa|VEVEKGVLPQLE54E|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtagaagttgaaaaaggcgttttgcctcaacttgaa/gaa|VEVEKGVLPQLE54E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME) +NC_045512.2 457 . T TA 577.0 PASS DP=184;AF=0.114130;SB=0;DP4=100,63,14,7;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||gaa/Agaa|E65R?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|TA),FRAME_SHIFT(HIGH||gaa/Agaa|E65R?|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|TA|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||gaa/Agaa|E65R?|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|TA|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||gaa/Agaa|E65R?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|TA);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 518 . ATGGTT A 126.0 min_af_0.050000 DP=553;AF=0.010850;SB=0;DP4=262,283,3,3;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||atggtt/|MV85|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),FRAME_SHIFT(HIGH||atggtt/|MV85|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||atggtt/|MV85|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||atggtt/|MV85|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 3037 . C T 4542.0 PASS DP=127;AF=0.960630;SB=0;DP4=0,0,70,57;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4291 . A G 83.0 min_af_0.050000 DP=220;AF=0.031818;SB=11;DP4=122,88,2,6;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1342|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1342|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A524|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A524|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 6373 . GGATA G 92.0 min_af_0.050000 DP=238;AF=0.016807;SB=0;DP4=123,111,2,2;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||gataat/|DN2037|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),FRAME_SHIFT(HIGH||gataat/|DN2037|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),FRAME_SHIFT(HIGH||gataat/|DN1219|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||gataat/|DN1219|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 6906 . C T 6592.0 PASS DP=175;AF=0.988571;SB=0;DP4=0,0,69,106;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2214L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2214L|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S1396L|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S1396L|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 10450 . C T 161.0 min_af_0.050000 DP=302;AF=0.046358;SB=0;DP4=178,105,9,5;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P3395|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P3395|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P132|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P132|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 10451 . A G 110.0 min_af_0.050000 DP=233;AF=0.047210;SB=19;DP4=161,55,4,7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N3396D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N3396D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N133D|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N133D|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 10620 . A G 239.0 PASS DP=347;AF=0.051873;SB=2;DP4=139,189,9,9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q3452R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q3452R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q189R|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q189R|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12835 . T G 115.0 min_af_0.050000 DP=423;AF=0.023641;SB=0;DP4=180,232,5,6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaG|D4190E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaG|D4190E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaG|D50E|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaG|D50E|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13123 . T C 163.0 min_af_0.050000 DP=775;AF=0.015484;SB=4;DP4=312,451,3,9;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S4286|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S4286|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S33|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S33|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13129 . A G 134.0 min_af_0.050000 DP=389;AF=0.048843;SB=0;DP4=165,197,9,11;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13815 . A G 95.0 min_af_0.050000 DP=551;AF=0.014519;SB=0;DP4=246,297,4,4;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A4517|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A125|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14408 . C T 6433.0 PASS DP=186;AF=0.962366;SB=0;DP4=1,1,96,86;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4715L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P323L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15324 . C T 9790.0 PASS DP=273;AF=0.992674;SB=0;DP4=0,0,140,133;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N5020|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N628|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 18108 . A G 72.0 min_af_0.050000 DP=376;AF=0.015957;SB=3;DP4=211,158,2,4;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A5948|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A23|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 22487 . GA G 64.0 min_af_0.050000 DP=200;AF=0.015000;SB=0;DP4=101,100,1,2;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||aaa/|K310|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 22573 . T C 71.0 min_af_0.050000 DP=256;AF=0.015625;SB=0;DP4=122,130,2,2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P337|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 23403 . A G 14383.0 PASS DP=391;AF=0.969309;SB=0;DP4=0,0,227,164;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G) +NC_045512.2 24108 . T C 71.0 min_af_0.050000 DP=410;AF=0.014634;SB=3;DP4=210,192,2,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L849P|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512.2 25207 . C T 152.0 min_af_0.050000 DP=307;AF=0.026059;SB=2;DP4=148,151,5,3;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1215|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512.2 25453 . A C 106.0 min_af_0.050000 DP=291;AF=0.020619;SB=1;DP4=139,144,4,3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Cag|K21Q|275|ORF3a|protein_coding|CODING|GU280_gp03|1|C) +NC_045512.2 29270 . TAC T 72.0 min_af_0.050000 DP=813;AF=0.004920;SB=0;DP4=450,363,2,2;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||aca/|T334|419|N|protein_coding|CODING|GU280_gp10|1|T|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00) +NC_045512.2 29564 . T G 81.0 min_af_0.050000 DP=762;AF=0.010499;SB=5;DP4=424,325,3,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Gat|Y3D|38|ORF10|protein_coding|CODING|GU280_gp11|1|G) +NC_045512.2 29765 . T C 370.0 min_af_0.050000 DP=581;AF=0.034423;SB=1;DP4=291,267,9,11
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snpeff.456.vcf Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,56 @@ +##fileformat=VCFv4.0 +##fileDate=20200707 +##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-14951 -o /data/dnb02/galaxy_db/job_working_directory/009/430/9430165/working/pp-tmp/lofreq2_call_parallel147y6wii/0.vcf.gz reads.bam +##reference=reference.fa +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> +##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> +##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant)."> +##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> +##FILTER=<ID=min_snvqual_66,Description="Minimum SNV Quality (Phred) 66"> +##FILTER=<ID=min_indelqual_51,Description="Minimum Indel Quality (Phred) 51"> +##FILTER=<ID=min_snvqual_70,Description="Minimum SNV Quality (Phred) 70"> +##FILTER=<ID=min_indelqual_56,Description="Minimum Indel Quality (Phred) 56"> +##FILTER=<ID=min_af_0.050000,Description="Minimum allele frequency 0.050000"> +##FILTER=<ID=min_dp_5,Description="Minimum Coverage 5"> +##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000"> +##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani" +##SnpEffCmd="SnpEff -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -no-utr -stats /data/dnb02/galaxy_db/job_working_directory/009/430/9430171/galaxy_dataset_24243787.dat NC_045512.2 /data/dnb02/galaxy_db/files/022/094/dataset_22094490.dat " +##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype [ | ERRORS | WARNINGS ] )' "> +##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +#CHROM POS ID REF ALT QUAL FILTER INFO +NC_045512.2 222 . C T 292.0 min_af_0.050000 DP=304;AF=0.046053;SB=1;DP4=130,160,7,7 +NC_045512.2 241 . C T 11451.0 PASS DP=311;AF=0.983923;SB=0;DP4=0,0,138,171 +NC_045512.2 520 . GGTT G 83.0 min_af_0.050000 DP=424;AF=0.009434;SB=0;DP4=216,206,2,2;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttgag/gag|VE86E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttgag/gag|VE86E|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttgag/gag|VE86E|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttgag/gag|VE86E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME) +NC_045512.2 1059 . C T 6195.0 PASS DP=201;AF=0.860696;SB=0;DP4=12,14,83,92;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T265I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T265I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T85I|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T85I|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 3037 . C T 4662.0 PASS DP=124;AF=0.983871;SB=0;DP4=0,0,63,61;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 3307 . G A 124.0 min_af_0.050000 DP=353;AF=0.019830;SB=1;DP4=245,101,6,1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M1014I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M1014I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M196I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M196I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 3373 . C A 3249.0 PASS DP=732;AF=0.166667;SB=1;DP4=288,319,57,68;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D1036E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D1036E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D218E|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D218E|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4456 . C T 79.0 min_af_0.050000 DP=476;AF=0.010504;SB=0;DP4=203,268,2,3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1397|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1397|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A579|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A579|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5138 . G T 154.0 min_af_0.050000 DP=506;AF=0.017787;SB=0;DP4=226,270,5,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Tac|D1625Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Tac|D1625Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Tac|D807Y|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Tac|D807Y|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 7388 . GC G 86.0 min_af_0.050000 DP=223;AF=0.017937;SB=0;DP4=103,117,2,2;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ccg/|P2376|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ccg/|P2376|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ccg/|P1558|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ccg/|P1558|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 10620 . A G 185.0 min_af_0.050000 DP=290;AF=0.048276;SB=0;DP4=126,150,6,8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q3452R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q3452R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q189R|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q189R|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13123 . T C 225.0 min_af_0.050000 DP=764;AF=0.019634;SB=0;DP4=302,446,7,9;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S4286|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S4286|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S33|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S33|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13129 . A G 145.0 PASS DP=395;AF=0.055696;SB=1;DP4=167,195,9,13;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 14408 . C T 7389.0 PASS DP=202;AF=0.995049;SB=0;DP4=0,0,103,99;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4715L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P323L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15380 . G T 276.0 min_af_0.050000 DP=286;AF=0.045455;SB=1;DP4=132,141,7,6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aTc|S5039I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aTc|S647I|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15385 . TCA T 90.0 min_af_0.050000 DP=292;AF=0.013699;SB=0;DP4=141,147,2,2;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||cac/|H5042|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||cac/|H650|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 15689 . G A 2771.0 PASS DP=273;AF=0.344322;SB=0;DP4=113,65,61,34;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R5142H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R750H|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 23403 . A G 10124.0 PASS DP=285;AF=0.943860;SB=0;DP4=0,0,166,119;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G) +NC_045512.2 24826 . CT C 83.0 min_af_0.050000 DP=451;AF=0.008869;SB=0;DP4=232,216,2,2;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||ttt/|F1089|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 25563 . G T 4454.0 PASS DP=173;AF=0.751445;SB=0;DP4=21,20,64,68;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q57H|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) +NC_045512.2 26259 . TTCGGAAGAGACAGGTACGTTAATA T 1183.0 PASS DP=201;AF=0.184080;SB=0;DP4=97,112,17,20;INDEL;HRUN=3;EFF=CODON_DELETION(MODERATE||tcggaagagacaggtacgttaata/|SEETGTLI6|75|E|protein_coding|CODING|GU280_gp04|1|T) +NC_045512.2 26753 . C T 137.0 min_af_0.050000 DP=592;AF=0.016892;SB=0;DP4=314,267,6,5;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T77|222|M|protein_coding|CODING|GU280_gp05|1|T) +NC_045512.2 27883 . C A 7166.0 PASS DP=413;AF=0.554479;SB=2;DP4=84,94,118,117;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gAc|A43D|43|ORF7b|protein_coding|CODING|GU280_gp08|1|A) +NC_045512.2 27916 . G T 1336.0 PASS DP=374;AF=0.139037;SB=6;DP4=147,173,30,24;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G8V|121|ORF8|protein_coding|CODING|GU280_gp09|1|T) +NC_045512.2 28134 . G GT 80.0 min_af_0.050000 DP=531;AF=0.007533;SB=0;DP4=295,232,2,2;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||tcc/tTcc|S82F?|121|ORF8|protein_coding|CODING|GU280_gp09|1|GT|INFO_REALIGN_3_PRIME);LOF=(ORF8|GU280_gp09|1|1.00) +NC_045512.2 28254 . A C 139.0 min_af_0.050000 DP=618;AF=0.017799;SB=2;DP4=297,309,7,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Ctc|I121L|121|ORF8|protein_coding|CODING|GU280_gp09|1|C) +NC_045512.2 28881 . G A 925.0 PASS DP=368;AF=0.108696;SB=0;DP4=159,166,21,21;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 28882 . G A 929.0 PASS DP=391;AF=0.104859;SB=0;DP4=175,174,21,21;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512.2 28883 . G C 945.0 PASS DP=391;AF=0.107417;SB=0;DP4=177,172,21,21;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C) +NC_045512.2 29659 . C T 70.0 min_af_0.050000 DP=1375;AF=0.004364;SB=0;DP4=614,755,3,3;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N34|38|ORF10|protein_coding|CODING|GU280_gp11|1|T) +NC_045512.2 29800 . G A 629.0 PASS DP=505;AF=0.057426;SB=0;DP4=245,229,16,13 +NC_045512.2 29859 . T C 80.0 min_af_0.050000 DP=299;AF=0.016722;SB=20;DP4=129,164,6,0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snpeff.789.vcf Wed Dec 02 21:23:06 2020 +0000 @@ -0,0 +1,50 @@ +##fileformat=VCFv4.0 +##fileDate=20200707 +##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-14951 -o /data/dnb02/galaxy_db/job_working_directory/009/430/9430167/working/pp-tmp/lofreq2_call_paralleleu47zedc/0.vcf.gz reads.bam +##reference=reference.fa +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> +##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> +##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant)."> +##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> +##FILTER=<ID=min_snvqual_64,Description="Minimum SNV Quality (Phred) 64"> +##FILTER=<ID=min_indelqual_47,Description="Minimum Indel Quality (Phred) 47"> +##FILTER=<ID=min_snvqual_68,Description="Minimum SNV Quality (Phred) 68"> +##FILTER=<ID=min_indelqual_53,Description="Minimum Indel Quality (Phred) 53"> +##FILTER=<ID=min_af_0.050000,Description="Minimum allele frequency 0.050000"> +##FILTER=<ID=min_dp_5,Description="Minimum Coverage 5"> +##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000"> +##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani" +##SnpEffCmd="SnpEff -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -no-utr -stats /data/dnb02/galaxy_db/job_working_directory/009/430/9430173/galaxy_dataset_24243791.dat NC_045512.2 /data/dnb02/galaxy_db/files/022/094/dataset_22094492.dat " +##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype [ | ERRORS | WARNINGS ] )' "> +##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +#CHROM POS ID REF ALT QUAL FILTER INFO +NC_045512.2 241 . C T 7565.0 PASS DP=202;AF=1.000000;SB=0;DP4=0,0,94,108 +NC_045512.2 3037 . C T 2399.0 PASS DP=64;AF=0.984375;SB=0;DP4=0,0,33,31;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 4291 . A G 87.0 PASS DP=127;AF=0.055118;SB=1;DP4=68,52,3,4;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1342|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1342|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A524|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A524|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 5806 . C T 203.0 min_af_0.050000 DP=260;AF=0.038462;SB=1;DP4=172,78,8,2;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C1847|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C1847|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C1029|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C1029|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 8554 . T C 95.0 PASS DP=116;AF=0.068966;SB=0;DP4=57,51,4,4;EFF=SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G1945|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G1945|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G2763|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G2763|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C) +NC_045512.2 10620 . A G 78.0 min_af_0.050000 DP=214;AF=0.028037;SB=0;DP4=88,120,2,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q3452R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q3452R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q189R|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q189R|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 12297 . A G 118.0 min_af_0.050000 DP=314;AF=0.028662;SB=0;DP4=131,174,4,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q4011R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q4011R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q69R|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q69R|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13123 . T C 186.0 min_af_0.050000 DP=573;AF=0.020942;SB=0;DP4=241,319,6,7;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S4286|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S4286|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S33|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S33|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13129 . A G 78.0 min_af_0.050000 DP=283;AF=0.035336;SB=2;DP4=126,144,4,7;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 13993 . G T 215.0 PASS DP=99;AF=0.090909;SB=11;DP4=60,30,3,6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A4577S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A185S|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 15830 . CA C 74.0 min_af_0.050000 DP=587;AF=0.006814;SB=0;DP4=256,327,2,2;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||aaa/|K5190|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K798|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 15958 . G A 73.0 min_af_0.050000 DP=148;AF=0.027027;SB=2;DP4=92,52,2,2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A5232T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A840T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 16695 . T G 117.0 min_af_0.050000 DP=202;AF=0.029703;SB=0;DP4=93,103,3,3;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acG|T5477|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|acT/acG|T153|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 17999 . C T 1226.0 PASS DP=483;AF=0.103520;SB=3;DP4=195,236,26,25;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T5912I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T588I|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 18108 . A G 74.0 min_af_0.050000 DP=193;AF=0.031088;SB=1;DP4=108,79,3,3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A5948|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A23|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 21147 . T C 77.0 min_af_0.050000 DP=150;AF=0.026667;SB=0;DP4=77,69,2,2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L6961|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L163|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON) +NC_045512.2 23403 . A G 8550.0 PASS DP=229;AF=0.982533;SB=0;DP4=0,0,136,93;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G) +NC_045512.2 23582 . TATCAGACTCAGACTA T 238.0 min_af_0.050000 DP=448;AF=0.022321;SB=2;DP4=177,263,5,5;INDEL;HRUN=1;EFF=CODON_DELETION(MODERATE||cagactcagactaat/|QTQTN675|1273|S|protein_coding|CODING|GU280_gp02|1|T|INFO_REALIGN_3_PRIME) +NC_045512.2 23595 . CTAATTCTCCTCGGCGGGCACG C 571.0 PASS DP=408;AF=0.051471;SB=4;DP4=167,227,11,10;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattctcctcggcgggcacgtagt/agt|NSPRRARS679S|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME) +NC_045512.2 26256 . CGTTTCGGAAGAGACAGGTACGTTAATA C 963.0 PASS DP=196;AF=0.153061;SB=1;DP4=76,90,12,18;INDEL;HRUN=1;EFF=CODON_DELETION(MODERATE||tcggaagagacaggtacgttaatagtt/|SEETGTLIV6|75|E|protein_coding|CODING|GU280_gp04|1|C|INFO_REALIGN_3_PRIME) +NC_045512.2 26259 . TTCGGAAGAGACAGGTACGTTAATA T 2451.0 PASS DP=133;AF=0.511278;SB=1;DP4=57,69,29,39;INDEL;HRUN=3;EFF=CODON_DELETION(MODERATE||tcggaagagacaggtacgttaata/|SEETGTLI6|75|E|protein_coding|CODING|GU280_gp04|1|T) +NC_045512.2 26895 . C T 240.0 min_af_0.050000 DP=557;AF=0.025135;SB=0;DP4=246,297,6,8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H125Y|222|M|protein_coding|CODING|GU280_gp05|1|T) +NC_045512.2 28868 . C T 446.0 PASS DP=236;AF=0.084746;SB=0;DP4=101,115,10,10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P199S|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512.2 29361 . TC T 71.0 min_af_0.050000 DP=862;AF=0.004640;SB=0;DP4=424,456,2,2;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||cca/|P364|419|N|protein_coding|CODING|GU280_gp10|1|T|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00) +NC_045512.2 29855 . T C 212.0 PASS DP=183;AF=0.054645;SB=1;DP4=89,84,6,4 +NC_045512.2 29859 . T C 72.0 min_af_0.050000 DP=164;AF=0.024390;SB=12;DP4=77,82,4,0