# HG changeset patch
# User ben-warren
# Date 1400805019 14400
# Node ID b321e0517be3ac3a65f01bf6bf963253bb85c7c3
# Parent  be070a68521ebdd66d89da402a30c2fd634b8d20
Uploaded

diff -r be070a68521e -r b321e0517be3 CAPS2gff.sh
--- a/CAPS2gff.sh	Thu Oct 18 19:47:07 2012 -0400
+++ b/CAPS2gff.sh	Thu May 22 20:30:19 2014 -0400
@@ -1,5 +1,7 @@
 #!/bin/sh
 ##convert output of CAPS detection tool to GFF3
+## usage 
+# sh CAPS2gff.sh <input tabular CAPS output> <output file>
 #Copyright 2012 John McCallum
 #New Zealand Institute for Plant and Food Research
 
diff -r be070a68521e -r b321e0517be3 Galaxy-Workflow-CAPS_Marker_Design_from_VCF.ga
--- a/Galaxy-Workflow-CAPS_Marker_Design_from_VCF.ga	Thu Oct 18 19:47:07 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,273 +0,0 @@
-{
-    "a_galaxy_workflow": "true", 
-    "annotation": "", 
-    "format-version": "0.1", 
-    "name": "CAPS Marker Design from VCF", 
-    "steps": {
-        "0": {
-            "annotation": "", 
-            "id": 0, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "", 
-                    "name": "Input Multi fasta Dataset"
-                }
-            ], 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 214, 
-                "top": 225
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"Input Multi fasta Dataset\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": []
-        }, 
-        "1": {
-            "annotation": "", 
-            "id": 1, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "", 
-                    "name": "Input VCF  Dataset"
-                }
-            ], 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 174, 
-                "top": 592
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"Input VCF  Dataset\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": []
-        }, 
-        "2": {
-            "annotation": "", 
-            "id": 2, 
-            "input_connections": {
-                "inputVcf": {
-                    "id": 1, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Convert vcf to gff", 
-            "outputs": [
-                {
-                    "name": "outputfile", 
-                    "type": "gff3"
-                }
-            ], 
-            "position": {
-                "left": 460.99998474121094, 
-                "top": 568
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/vcf2gff_1/1.0.0", 
-            "tool_state": "{\"inputVcf\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "3": {
-            "annotation": "Detect resitriction polymorphisms", 
-            "id": 3, 
-            "input_connections": {
-                "inputFasta": {
-                    "id": 0, 
-                    "output_name": "output"
-                }, 
-                "inputSNPGff3File": {
-                    "id": 2, 
-                    "output_name": "outputfile"
-                }
-            }, 
-            "inputs": [], 
-            "name": "CAPS Detection", 
-            "outputs": [
-                {
-                    "name": "outputfile", 
-                    "type": "interval"
-                }
-            ], 
-            "position": {
-                "left": 646.99998474121094, 
-                "top": 382
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/CAPS_Marker_Design_2/1.0.0", 
-            "tool_state": "{\"inputFasta\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputSNPGff3File\": \"null\", \"__page__\": 0}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "4": {
-            "annotation": "get feature ID column", 
-            "id": 4, 
-            "input_connections": {
-                "input": {
-                    "id": 3, 
-                    "output_name": "outputfile"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Cut", 
-            "outputs": [
-                {
-                    "name": "out_file1", 
-                    "type": "tabular"
-                }
-            ], 
-            "position": {
-                "left": 892, 
-                "top": 415
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "Cut1", 
-            "tool_state": "{\"columnList\": \"\\\"c4\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
-            "tool_version": "1.0.1", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "5": {
-            "annotation": "", 
-            "id": 5, 
-            "input_connections": {
-                "inputSNPfile": {
-                    "id": 2, 
-                    "output_name": "outputfile"
-                }, 
-                "inputTargetfile": {
-                    "id": 4, 
-                    "output_name": "out_file1"
-                }, 
-                "inputfastaFile": {
-                    "id": 0, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Design primers to features", 
-                    "name": "min_size"
-                }, 
-                {
-                    "description": "runtime parameter for tool Design primers to features", 
-                    "name": "max_size"
-                }
-            ], 
-            "name": "Design primers to features", 
-            "outputs": [
-                {
-                    "name": "primer_outputfile", 
-                    "type": "tabular"
-                }
-            ], 
-            "position": {
-                "left": 1186, 
-                "top": 382
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionprimer_outputfile": {
-                    "action_arguments": {
-                        "newname": "PrimerPairs"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "primer_outputfile"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/Genetic_Marker_Design_2/1.0.0", 
-            "tool_state": "{\"__page__\": 0, \"inputTargetfile\": \"null\", \"inputfastaFile\": \"null\", \"min_size\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"inputSNPfile\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"max_size\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "6": {
-            "annotation": "", 
-            "id": 6, 
-            "input_connections": {
-                "input": {
-                    "id": 5, 
-                    "output_name": "primer_outputfile"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Select", 
-            "outputs": [
-                {
-                    "name": "out_file1", 
-                    "type": "input"
-                }
-            ], 
-            "position": {
-                "left": 1406, 
-                "top": 382
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionout_file1": {
-                    "action_arguments": {
-                        "newname": "SuccessfulDesignSets"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "out_file1"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "Grep1", 
-            "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"true\\\"\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"pattern\": \"\\\"NONE\\\"\"}", 
-            "tool_version": "1.0.1", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "7": {
-            "annotation": "", 
-            "id": 7, 
-            "input_connections": {
-                "inputFile": {
-                    "id": 6, 
-                    "output_name": "out_file1"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Unique", 
-            "outputs": [
-                {
-                    "name": "outputfile", 
-                    "type": "txt"
-                }
-            ], 
-            "position": {
-                "left": 1625.9999389648438, 
-                "top": 382
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionoutputfile": {
-                    "action_arguments": {
-                        "newname": "UniquePrimerSets"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outputfile"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/uni_Mask_1/1.0.0", 
-            "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }
-    }
-}
\ No newline at end of file
diff -r be070a68521e -r b321e0517be3 Galaxy-Workflow-CAPS_Marker_Development_from_454_Read_Mapping.ga
--- a/Galaxy-Workflow-CAPS_Marker_Development_from_454_Read_Mapping.ga	Thu Oct 18 19:47:07 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,401 +0,0 @@
-{
-    "a_galaxy_workflow": "true", 
-    "annotation": "", 
-    "format-version": "0.1", 
-    "name": "CAPS Marker Development from 454 Read Mapping", 
-    "steps": {
-        "0": {
-            "annotation": "", 
-            "id": 0, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "", 
-                    "name": "Reference sequences"
-                }
-            ], 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 122.80303955078125, 
-                "top": 119.77274131774902
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"Reference sequences\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": []
-        }, 
-        "1": {
-            "annotation": "Reads to map", 
-            "id": 1, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "Reads to map", 
-                    "name": "SFF File "
-                }
-            ], 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 104.6212158203125, 
-                "top": 313.95454406738281
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"SFF File \"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": []
-        }, 
-        "2": {
-            "annotation": "barcode, vector or adapter sequences to trim", 
-            "id": 2, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "barcode, vector or adapter sequences to trim", 
-                    "name": "Trimming file"
-                }
-            ], 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 195.727294921875, 
-                "top": 544.8787841796875
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"Trimming file\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": []
-        }, 
-        "3": {
-            "annotation": "", 
-            "id": 3, 
-            "input_connections": {
-                "ref_inputs_0|ref_input": {
-                    "id": 0, 
-                    "output_name": "output"
-                }, 
-                "sff_inputs_0|sff_input": {
-                    "id": 1, 
-                    "output_name": "output"
-                }, 
-                "vt": {
-                    "id": 2, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [], 
-            "name": "runMapping", 
-            "outputs": [
-                {
-                    "name": "newbler_metrics", 
-                    "type": "txt"
-                }, 
-                {
-                    "name": "read_status", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "trimmed_reads_fasta", 
-                    "type": "fasta"
-                }, 
-                {
-                    "name": "trimmed_reads_qual", 
-                    "type": "qual454"
-                }, 
-                {
-                    "name": "alignment_info", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "all_contigs_fasta", 
-                    "type": "fasta"
-                }, 
-                {
-                    "name": "all_contigs_qual", 
-                    "type": "qual454"
-                }, 
-                {
-                    "name": "contigs_ace", 
-                    "type": "ace"
-                }, 
-                {
-                    "name": "large_contigs_fasta", 
-                    "type": "fasta"
-                }, 
-                {
-                    "name": "large_contigs_qual", 
-                    "type": "qual454"
-                }, 
-                {
-                    "name": "pair_align", 
-                    "type": "txt"
-                }, 
-                {
-                    "name": "pair_status", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "scaffolds_fasta", 
-                    "type": "fasta"
-                }, 
-                {
-                    "name": "scaffolds_qual", 
-                    "type": "qual454"
-                }, 
-                {
-                    "name": "scaffolds_agp", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "tag_pair_align", 
-                    "type": "txt"
-                }, 
-                {
-                    "name": "trim_status", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "all_diffs", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "all_struct_vars", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "hc_diff", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "hc_struct_vars", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "gene_status", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "mapping_qc", 
-                    "type": "xls"
-                }, 
-                {
-                    "name": "ref_status", 
-                    "type": "tabular"
-                }
-            ], 
-            "position": {
-                "left": 432.71212768554688, 
-                "top": 330.90908813476562
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/edward-kirton/roche454_toolsuite/runMapping/1.0.1", 
-            "tool_state": "{\"minlen\": \"\\\"20\\\"\", \"rst\": \"\\\"12\\\"\", \"vs\": \"null\", \"vt\": \"null\", \"__page__\": 0, \"no\": \"\\\"\\\"\", \"paired_reads\": \"\\\"false\\\"\", \"notrim\": \"\\\"False\\\"\", \"tr\": \"\\\"-tr\\\"\", \"mcf\": \"null\", \"ref_type\": \"\\\"-gref\\\"\", \"newbler_exe\": \"\\\"runMapping\\\"\", \"info\": \"\\\"-info\\\"\", \"sanger_inputs\": \"[]\", \"sl\": \"\\\"16\\\"\", \"hsl\": \"\\\"70\\\"\", \"sanger_paired_inputs\": \"[]\", \"fe\": \"null\", \"pair\": \"\\\"\\\"\", \"fi\": \"null\", \"nor\": \"\\\"False\\\"\", \"a\": \"\\\"100\\\"\", \"sff_paired_inputs\": \"[]\", \"e\": \"\\\"0\\\"\", \"ace\": \"\\\"\\\"\", \"ss\": \"\\\"12\\\"\", \"ml\": \"\\\"40\\\"\", \"mi\": \"\\\"90\\\"\", \"l\": \"\\\"500\\\"\", \"ais\": \"\\\"2\\\"\", \"ref_inputs\": \"[{\\\"__index__\\\": 0, \\\"ref_input\\\": null}]\", \"srv\": \"\\\"False\\\"\", \"sff_inputs\": \"[{\\\"__index__\\\": 0, \\\"sff_input\\\": null}]\", \"sc\": \"\\\"1\\\"\", \"ud\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"qo\": \"\\\"False\\\"\"}", 
-            "tool_version": "1.0.1", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "4": {
-            "annotation": "", 
-            "id": 4, 
-            "input_connections": {
-                "inputGsFile": {
-                    "id": 3, 
-                    "output_name": "all_diffs"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Convert gsMapper to gff3", 
-            "outputs": [
-                {
-                    "name": "outputfile", 
-                    "type": "gff3"
-                }
-            ], 
-            "position": {
-                "left": 729.65148448944092, 
-                "top": 503.80300903320312
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/gsMapper_to_gff3_1/1.0.0", 
-            "tool_state": "{\"__page__\": 0, \"inputGsFile\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "5": {
-            "annotation": "", 
-            "id": 5, 
-            "input_connections": {
-                "inputFasta": {
-                    "id": 0, 
-                    "output_name": "output"
-                }, 
-                "inputSNPGff3File": {
-                    "id": 4, 
-                    "output_name": "outputfile"
-                }
-            }, 
-            "inputs": [], 
-            "name": "CAPS Detection", 
-            "outputs": [
-                {
-                    "name": "outputfile", 
-                    "type": "interval"
-                }
-            ], 
-            "position": {
-                "left": 994.77265930175781, 
-                "top": 317.83332824707031
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/CAPS_Marker_Design_2/1.0.0", 
-            "tool_state": "{\"inputFasta\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputSNPGff3File\": \"null\", \"__page__\": 0}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "6": {
-            "annotation": "", 
-            "id": 6, 
-            "input_connections": {
-                "input": {
-                    "id": 5, 
-                    "output_name": "outputfile"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Cut", 
-            "outputs": [
-                {
-                    "name": "out_file1", 
-                    "type": "tabular"
-                }
-            ], 
-            "position": {
-                "left": 1222.7424011230469, 
-                "top": 314.98484802246094
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "Cut1", 
-            "tool_state": "{\"columnList\": \"\\\"c4\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
-            "tool_version": "1.0.1", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "7": {
-            "annotation": "", 
-            "id": 7, 
-            "input_connections": {
-                "inputSNPfile": {
-                    "id": 4, 
-                    "output_name": "outputfile"
-                }, 
-                "inputTargetfile": {
-                    "id": 6, 
-                    "output_name": "out_file1"
-                }, 
-                "inputfastaFile": {
-                    "id": 0, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Design primers to features", 
-                    "name": "min_size"
-                }, 
-                {
-                    "description": "runtime parameter for tool Design primers to features", 
-                    "name": "max_size"
-                }
-            ], 
-            "name": "Design primers to features", 
-            "outputs": [
-                {
-                    "name": "primer_outputfile", 
-                    "type": "tabular"
-                }
-            ], 
-            "position": {
-                "left": 1442.6968994140625, 
-                "top": 314.98484802246094
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/Genetic_Marker_Design_2/1.0.0", 
-            "tool_state": "{\"__page__\": 0, \"inputTargetfile\": \"null\", \"inputfastaFile\": \"null\", \"min_size\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"inputSNPfile\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"max_size\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "8": {
-            "annotation": "Select successful design targets", 
-            "id": 8, 
-            "input_connections": {
-                "input": {
-                    "id": 7, 
-                    "output_name": "primer_outputfile"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Select", 
-            "outputs": [
-                {
-                    "name": "out_file1", 
-                    "type": "input"
-                }
-            ], 
-            "position": {
-                "left": 1692.6968994140625, 
-                "top": 316.92424011230469
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "Grep1", 
-            "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"true\\\"\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"pattern\": \"\\\"NONE\\\"\"}", 
-            "tool_version": "1.0.1", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "9": {
-            "annotation": "Remove duplicates", 
-            "id": 9, 
-            "input_connections": {
-                "inputFile": {
-                    "id": 8, 
-                    "output_name": "out_file1"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Unique", 
-            "outputs": [
-                {
-                    "name": "outputfile", 
-                    "type": "txt"
-                }
-            ], 
-            "position": {
-                "left": 1900.6818237304688, 
-                "top": 310.90907287597656
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/uni_Mask_1/1.0.0", 
-            "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }
-    }
-}
\ No newline at end of file
diff -r be070a68521e -r b321e0517be3 README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,24 @@
+galaxy-pcr-markers
+==================
+
+Scripts for design of PCR-based Marker Assays from DNA sequence variant data, and xml wrappers for use in  Galaxy  workflow environment 
+
+Also available for download at Galaxy Toolshed http://toolshed.g2.bx.psu.edu/
+hg clone http://toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers
+
+NOTE that the primer design tool *design_primers.py*  relies on EMBOSS ePrimer3 which depends on Primer3 1.1.4.
+The updated tool *design_HRM_primers.py* does not have this restriction and should work with Primer3 V2.
+
+Please see development branch HRM for optimised design of high-resolution melting PCR assays using the uMelt web service at University of Utah.
+
+
+**CITATION**
+A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data: Application For Development Of A Framework Linkage Map In Bulb Onion (Allium cepa L.) (2012)
+
+Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum
+
+BMC Genomics 2012, 13:637  http://www.biomedcentral.com/1471-2164/13/637/abstract
+
+**Acknowledgements**
+Current development of these tools is funded by the New Zealand Ministry for Business, Innovation & Employment project 'Virtual Institute of Statistical Genetics' (VISG)
+See http://www.visg.co.nz
diff -r be070a68521e -r b321e0517be3 design_primers.py
--- a/design_primers.py	Thu Oct 18 19:47:07 2012 -0400
+++ b/design_primers.py	Thu May 22 20:30:19 2014 -0400
@@ -1,9 +1,13 @@
-#!/usr/local/bin/python2.6
-##design primers to features in multiple sequences
-##usage: python  design_primers.py <fasta-file> <gff file> <file of target IDs> <prod_min_size> <prod_max_size>
 
+#!/usr/bin/env python
+##design primers to features in multiple sequences, with option to predict melting
+#usage: design_HRM_primers.py [-h] -i IN_FILE -g GFF_FILE -T TARGET_FILE [-u]
+#                             [-n MAX_PRIMERS] [-p PROD_MIN_SIZE]
+#                             [-P PROD_MAX_SIZE] [-l OPT_PRIMER_LENGTH]
+#                             [-m MAX_TM_DIFF] [-t OPTIMUM_TM]
+#                             [-G OPT_GC_PERCENT] [-x MAXPOLYX] [-c GC_CLAMP]
 
-#Copyright 2012 John McCallum & Leshi Chen
+#Copyright 2013 John McCallum & Susan Thomson
 #New Zealand Institute for Plant and Food Research
 #This program is free software: you can redistribute it and/or modify
 #     it under the terms of the GNU General Public License as published by
@@ -18,44 +22,86 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-
 import os
 import StringIO
 import re
-import tempfile
-import subprocess
 import copy
 import sys
 from BCBio import GFF
 from BCBio.GFF import GFFExaminer
 from Bio import SeqIO
-from Bio.Emboss.Applications import Primer3Commandline
-from Bio.Emboss import Primer3
+import run_p3 as P3
+#import umelt_service as umelts
+import argparse	
+
+##Primer3 defaults or additional options defined as dictionary 
+def_dict={
+'PRIMER_MIN_SIZE':'18',
+'PRIMER_MAX_SIZE':'25',
+'PRIMER_MAX_NS_ACCEPTED':'1'}
+
+#parse arguments
+parser = argparse.ArgumentParser(description='Primer set design and melt prediction parameters')
+parser.add_argument('-i', type=argparse.FileType('r'), help="input sequence file, required", dest='in_file', required=True)
+parser.add_argument('-g', type=argparse.FileType('r'), help="input gff file with SNP and indels, required", dest='gff_file', required=True)
+parser.add_argument('-T', type=argparse.FileType('r'), help="input target SNP file, required", dest='target_file', required=True)
+parser.add_argument('-u',help="do uMelt prediction, optional", dest='run_uMelt',action='store_true', default=False )
+parser.add_argument('-n', type=int, help="maximum number of primer pairs to return, default=5", dest='max_primers', default=5) ## PRIMER_NUM_RETURN
+parser.add_argument('-p', type=int, help="minimum product size", dest='prod_min_size', default=100)                             ## PRIMER_PRODUCT_SIZE_RANGE min
+parser.add_argument('-P', type=int, help="maximum product size", dest='prod_max_size', default=300)                            ## PRIMER_PRODUCT_SIZE_RANGE max
+parser.add_argument('-l', type=int, help="optimum primer length", dest='opt_primer_length', default=20)                        ## PRIMER_OPT_SIZE
+parser.add_argument('-m', type=int, help="maximum tm difference between primers", dest='max_tm_diff', default=1)               ## PRIMER_PAIR_MAX_DIFF_TM
+parser.add_argument('-t', type=int, help="optimum Tm for primers, recommend range 59 to 61", dest='optimum_tm', default=59)    ## PRIMER_OPT_TM
+parser.add_argument('-G', type=int, help="optimum GC percentage of primers", dest='opt_GC_percent', default=50)                ## PRIMER_OPT_GC_PERCENT
+parser.add_argument('-x', type=int, help="maximum polyx, recommend less than 4", dest='maxpolyx', default=3)                   ## PRIMER_MAX_POLY_X
+parser.add_argument('-c', type=int, help="number of C/Gs at end, recommend 2", dest='gc_clamp', default=1)                     ## PRIMER_GC_CLAMP
+
+parser.add_argument('-e', type=int, help="maximum allowable 3'-anchored complementarity", dest='maxselfend', default=3)                     ## PRIMER_MAX_SELF_END
+parser.add_argument('-a', type=int, help="maximum complementarity between left and right or self", dest='maxselfany', default=8)                     ## PRIMER_MAX_SELF_ANY
+parser.add_argument('-maxgc', type=float, help="Maximum allowable percentage of Gs and Cs in any primer.", dest='maxgc', default=80.0)                     ## PRIMER_MAX_GC
+parser.add_argument('-mingc', type=float, help="Minimum allowable percentage of Gs and Cs in any primer.", dest='mingc', default=20.0)                     ## PRIMER_MIN_GC
 
 
-in_file = sys.argv[1]
-gff_file = sys.argv[2] 
-target_file =  sys.argv[3]
-prod_min_size = int(sys.argv[4])
-prod_max_size = int(sys.argv[5])
+parser.add_argument('-d', type=str, help="variant indentifier delimiter, used to separate sequence ID from rest ", dest='target_delim', default=':')                      
+try:
+        my_args = parser.parse_args()  
+except SystemExit:
+        print("\nOops, an argument is missing/invalid, exiting...\n")
+        sys.exit(0)
+
+##update from args. NEEDS TO BE FINISHED
+productsizerange = str(my_args.prod_min_size) + "-" + str(my_args.prod_max_size)
+def_dict['PRIMER_PRODUCT_SIZE_RANGE']=productsizerange
+def_dict['PRIMER_NUM_RETURN']=str(my_args.max_primers +1)
+def_dict['PRIMER_OPT_SIZE']=str(my_args.opt_primer_length)
+def_dict['PRIMER_PAIR_MAX_DIFF_TM']=str(my_args.max_tm_diff)
+def_dict['PRIMER_OPT_TM']=str(my_args.optimum_tm)
+def_dict['PRIMER_OPT_GC_PERCENT']=str(my_args.opt_GC_percent)
+def_dict['PRIMER_MAX_POLY_X']=str(my_args.maxpolyx)
+def_dict['PRIMER_GC_CLAMP']=str(my_args.gc_clamp)
 
-max_tm_diff=1                                        ##
-opt_GC_percent=50                                    ##
-maxpolyx=4                                           ##
-optimum_length=20
-##target is specified in start, end format 
-productsizerange = str(prod_min_size) + "," + str(prod_max_size)
+def_dict['PRIMER_MAX_SELF_END']=str(my_args.maxselfend)
+def_dict['PRIMER_MAX_SELF_ANY']=str(my_args.maxselfany)
+def_dict['PRIMER_MAX_GC']=str(my_args.maxgc)
+def_dict['PRIMER_MIN_GC']=str(my_args.mingc)
+
+
+
+##conditional import of umelt
+if my_args.run_uMelt:
+    import umelt_service as umelts
+
 #open input files
-in_seq_handle = open(in_file)
-in_gff_handle = open(gff_file)
-in_target_handle=open(target_file)
-#read  target feature IDs into list
-targets=in_target_handle.readlines()
-in_target_handle.close()
+
+targets=my_args.target_file.readlines()
+my_args.target_file.close()
 ##and create a hit list of sequences from this
-target_seq_id_list = list(set([line.split(":")[0] for line in targets]))
+target_seq_id_list = [re.split(my_args.target_delim,X)[0] for X in targets] ## target_delimiter defaults to ':'  e.g. ABC:SNP:SAMTOOL:1234 
+
+##print header
+print "SNP_Target_ID", "Position","Ref_base","Variant_base" ,"Amplicon_bp","PRIMER_LEFT_SEQUENCE",'PRIMER_RIGHT_SEQUENCE', "ref_melt_Tm","var_melt_Tm","Tm_difference"
 ##create iterator returning sequence records
-for myrec in SeqIO.parse(in_seq_handle, "fasta"):
+for myrec in SeqIO.parse(my_args.in_file, "fasta"):
     #check if this sequence is included in the target list
     if myrec.id in target_seq_id_list:
         ##create sequence dictionary so we can add in gff annotations
@@ -63,9 +109,9 @@
         ##just limit to gff annotations for this sequence
         limit_info = dict(gff_id = [ myrec.id ])
         ##rewind gff filehandle
-        in_gff_handle.seek(0)
+        my_args.gff_file.seek(0)
         ##read annotations into sequence dictionary for this sequence record only 
-        annotations = [r for r in GFF.parse(in_gff_handle, base_dict=seq_dict,limit_info=limit_info)]
+        annotations = [r for r in GFF.parse(my_args.gff_file, base_dict=seq_dict,limit_info=limit_info)]
         ##if there are any annotations, then  proceed. 
         if annotations:
             rec=annotations[0]
@@ -75,79 +121,58 @@
                 target_annotations = [f for f in rec.features if f.id == target_ID ]
                 if target_annotations:
                     mytarget = target_annotations[0]
-                    #create temporary files
-                    tempfastaFile = tempfile.mktemp()
-                    tempproutfile = tempfile.mktemp()
                     #just consider slice of sequence in a window of +/- prod_max_size  bp
                     ##from feature UNLESS feature is close to end
                     ##Note that slice is zero-based
                     featLocation = mytarget.location.start.position 
-                    if featLocation > prod_max_size:
-                        slice_start = featLocation - prod_max_size
-                        featPosition = prod_max_size  
+                    if featLocation > my_args.prod_max_size:
+                        slice_start = featLocation -  my_args.prod_max_size
+                        featPosition =  my_args.prod_max_size  
                     else:
                         slice_start = 0
                         featPosition = featLocation
-                    if (len(rec) - featLocation) < prod_max_size:
+                    if (len(rec) - featLocation) <  my_args.prod_max_size:
                         slice_end = len(rec)
                     else:
-                        slice_end = featLocation + prod_max_size
+                        slice_end = featLocation +  my_args.prod_max_size
                     ###grab slice of sequence fom this window.
                     targetRec = rec[slice_start:slice_end]
                     matching_feature = [f for f in targetRec.features if f.id == mytarget.id]
                     if matching_feature:
                         target_feat = matching_feature[0]
+                        my_target_dict={} # re-initialize target dictionary
                         if target_feat.location.start.position == 0:
                             target_feat.location.start.position = 1
-                        #we get the mask features by removing the target...all features are masked as just using snp and indels
-                        ##a smarter filter could be added 
-                        ##note use of list copy to avoid possible side-effects
-                        exclude_feat = list(targetRec.features)
+                        #get the mask features by removing  target...all features are masked as just using snp and indels, a smarter filter could be added 
+			exclude_feat = list(targetRec.features) ##list copy to avoid possible side-effects
                         exclude_feat.remove(target_feat)
-                        ##print'targetRec.features',  targetRec.features ##for debug
-                        mask_str=map(lambda f: str(f.location.start.position+1) + "," + str(f.location.end.position + 1) ,exclude_feat)
-                        #mask_str=map(lambda f: str(f.location).strip('[]'),exclude_feat)
-                        p3_exclude_str = str(mask_str).replace('\', \'',':')
-                        p3_target = str(target_feat.location.start.position +1)  + "," + str(target_feat.location.end.position +1)
-                        #write sequence record into template file as  fasta
-                        t_output_handle = open(tempfastaFile, "w")
-                        SeqIO.write([targetRec], t_output_handle, "fasta")
-                        t_output_handle.close()
-                        #create Primer3Commandline() for emboss tool
-                        primer_cl = Primer3Commandline()
-                        #set the emboss tool to suppress  output as this will make Galaxy  think it is error message although it is a message to state run success
-                        primer_cl.set_parameter("-auto",'1')
-                        #pass  sequence file to emboss
-                        primer_cl.set_parameter("-sequence",tempfastaFile)
-                        #add target location
-                        primer_cl.set_parameter("-target", p3_target)
-                        ##mask off other features...dumb masking of everything at present, beware
-                        if (p3_exclude_str != ""):
-                            primer_cl.set_parameter("-excludedregion", p3_exclude_str)
-                        #add temporary output file to get the result
-                        primer_cl.set_parameter("-outfile", tempproutfile)
-                        #specify maximum different of tm
-                        primer_cl.set_parameter("-maxdifftm",max_tm_diff )
-                        #other useful parameters
-                        primer_cl.set_parameter("-ogcpercent", opt_GC_percent)
-                        primer_cl.set_parameter("-opolyxmax", maxpolyx)  
-                        primer_cl.set_parameter("-osize", optimum_length)
-                        #set product size range
-                        primer_cl.set_parameter("-prange", productsizerange)
-                        #using python subprocess method to run emboss command line programe with the parameters given
-                        fnull = open(os.devnull, 'w')
-                        result=subprocess.check_call(str(primer_cl),shell=True ,stdout = fnull, stderr = fnull)
-                        #read temporary outputfile
-                        handle = open(tempproutfile)
-                        record = Primer3.read(handle)
-                        ##just return first set, if there is one
-                        if len(record.primers) > 0:
-                            primer= record.primers[0]
-                            outputstr=[mytarget.id, primer.forward_seq,primer.reverse_seq,primer.size]
-                        else:
-                            outputstr=[mytarget.id,"NONE","NONE","NONE"]
-                        print('\t'.join(map(str,outputstr)))
+			excludes_str=' '.join([str(x.location.start.position)+','+str(x.location.end.position -x.location.start.position) for x in exclude_feat])
+                        my_target_dict={'SEQUENCE_ID' : rec.name, 'SEQUENCE_TEMPLATE': targetRec.seq.tostring(),'SEQUENCE_TARGET': str(target_feat.location.start.position) + ',1','SEQUENCE_INTERNAL_EXCLUDED_REGION': excludes_str}
+                        my_target_dict.update(def_dict) ##add in defaults
+			result=P3.run_P3(target_dict=my_target_dict)
+                        if my_args.run_uMelt:
+                            amp_seq=targetRec.seq ##need to make this conditional on getting a result >0 and melt=True
+                            mutamp_seq=targetRec.seq.tomutable()
+                            mutamp_seq[target_feat.location.start:target_feat.location.end]=target_feat.qualifiers['Variant_seq'][0] #mutate to variant
+			for primerset in result:
+				amp_start=int(primerset['PRIMER_LEFT'].split(',')[0])
+				amp_end=int(primerset['PRIMER_RIGHT'].split(',')[0])
+                                ref_melt_Tm=0
+                                var_melt_Tm=0
+                                if my_args.run_uMelt:
+                                    try:
+                                        ref_melt_Tm=umelts.getTm(umelts.getmelt(amp_seq.tostring()[amp_start:amp_end+1]))
+					var_melt_Tm=umelts.getTm(umelts.getmelt(mutamp_seq.tostring()[amp_start:amp_end+1]))
+                                    except:
+					ref_melt_Tm=0 ##preferably something more informative?
+					var_melt_Tm=0 ##exception handling to be added
+                                reference_seq=target_feat.qualifiers['Reference_seq'][0]
+                                if target_feat.qualifiers.has_key('Variant_seq'):
+                                    variant_seq=target_feat.qualifiers['Variant_seq'][0]
+                                else:
+                                    variant_seq="NA"
+                                print mytarget.id, featLocation + 1 ,reference_seq, variant_seq,amp_end-amp_start,primerset['PRIMER_LEFT_SEQUENCE'],primerset['PRIMER_RIGHT_SEQUENCE'], ref_melt_Tm,var_melt_Tm,abs(ref_melt_Tm-var_melt_Tm)#, amp_seq.tostring()[amp_start:amp_end+1], mutamp_seq.tostring()[amp_start:amp_end+1]
 
-                        
-in_gff_handle.close()
-in_seq_handle.close()
+my_args.gff_file.close()
+my_args.in_file.close()
+
diff -r be070a68521e -r b321e0517be3 design_primers.xml
--- a/design_primers.xml	Thu Oct 18 19:47:07 2012 -0400
+++ b/design_primers.xml	Thu May 22 20:30:19 2014 -0400
@@ -1,14 +1,25 @@
 <?xml version="1.0"?>
 <tool id="Genetic_Marker_Design_2" name="Design primers to features">
   <description>Design PCR Primers to Features</description>
-  <command interpreter="python">design_primers.py $inputfastaFile $inputSNPfile $inputTargetfile $min_size $max_size >  $primer_outputfile  </command>
+ <command interpreter="python -W ignore">
+      #if 'Yes' in $uMelt.value
+          design_primers.py -i $inputfastaFile -g $inputSNPfile -T $inputTargetfile -p $min_size -P $max_size -u >  $primer_outputfile
+      #else
+          design_primers.py -i $inputfastaFile -g $inputSNPfile -T $inputTargetfile -p $min_size -P $max_size  >  $primer_outputfile  
+      #end if
+       </command>
+
   <inputs>
     <param format="fasta" name="inputfastaFile" type="data" label="Multifasta Source file" />
     <param format="gff3" name="inputSNPfile" type="data" label="annotation file(Gff3)" />
     <param format="txt" name="inputTargetfile" type="data" optional="false" label="Target file" help="IN FORMAT Sequence id:source:type:start e.g. 1174806:gsMapper:SNP:292" ></param>
 <param name="min_size" size="20" type="text" value="75" label="Minimum Product Size Range" />
      <param name="max_size" size="20" type="text" value="100" label="Maximum Product Size Range" />
-  </inputs>
+ <param name="uMelt"  type="select"  label="uMelt prediction for HRM">
+            <option value="No" selected= "true">No</option>
+            <option value="Yes">Yes</option>
+         </param>
+ </inputs>
   <outputs>
      <data format="tabular"  name="primer_outputfile" />
   </outputs>
@@ -18,6 +29,7 @@
 **TIP**
 
 This tool designs primer pairs to flank features
+Optionally it can predict reference and variant Tm using the uMelt web service provided by University of Utah
 
 It takes 
 
diff -r be070a68521e -r b321e0517be3 find_CAPS.xml
--- a/find_CAPS.xml	Thu Oct 18 19:47:07 2012 -0400
+++ b/find_CAPS.xml	Thu May 22 20:30:19 2014 -0400
@@ -9,6 +9,13 @@
   <outputs>
      <data format="interval" name="outputfile" />
   </outputs>
+  <tests>
+        <test>
+                <param name="inputSNPGff3File" value="targets.gff" ftype="gff3"/>
+                <param name="inputFasta" value="targets.fasta" ftype="fasta"/>
+                <output name="outputfile" file="find_caps_output.txt"/>
+        </test>
+  </tests>
 <help>
 .. class:: infomark
 	
@@ -32,7 +39,7 @@
 
 
 
-*input GFF*
+*input GFF3*
 
 ::
 
diff -r be070a68521e -r b321e0517be3 gsmapper2gff.sh
--- a/gsmapper2gff.sh	Thu Oct 18 19:47:07 2012 -0400
+++ b/gsmapper2gff.sh	Thu May 22 20:30:19 2014 -0400
@@ -15,6 +15,8 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
+##usage gsmapper2gff.sh <input 454HCDiffs.txt or 454AllDiffs.txt file>  <output gff3 file>
+
 
 infile=$1
 outfile=$2
diff -r be070a68521e -r b321e0517be3 ipcress.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ipcress.xml	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,56 @@
+<?xml version="1.0"?>
+<tool id="ipcress" name="In-Silico PCR Experiment Simulation System">
+        <description>In-Silico PCR Experiment Simulation System</description>
+        <version_command>ipcress -v</version_command>
+        <command>
+                awk -v min=$min_length -v max=$max_length '{print $1,$2,$3, min, max}' $input_primers | ipcress -i /dev/stdin -s $input_seqs -m $mismatch $products_as_fasta $pretty -S $seed_length > $pcr_products
+        </command>
+        <inputs>
+                <param format="txt" name="input_primers" type="data" label="PCR Experiment Data" />
+                <param format="fasta" name="input_seqs" type="data" label="Sequences (Fasta)" />
+                <param name="mismatch" size="10" type="integer" value="0" label="Mismatches allowed per primer" />
+                <param name="min_length" size="10" type="integer" value="50" label="Minimum PCR product length" />
+                <param name="max_length" size="10" type="integer" value="100" label="Maximum PCR product length" />
+                <param name="products_as_fasta" type="boolean" truevalue="-P" falsevalue="" label="Display PCR products as a FASTA format sequence" />
+                <param name="pretty" type="boolean" truevalue="-p 1" falsevalue="-p 0" checked="true" label="Display Result in pretty format" />
+                <param name="seed_length" size="10" type="integer" value="12" label="Seed length: 0 => Use Full Primer Length" />
+        </inputs>
+        <outputs>
+                <data format="txt" name="pcr_products" />
+        </outputs>
+        <stdio>
+                <exit_code range="1:" level="fatal" description="Fatal Error" />
+        </stdio>
+        <tests>
+        <test>
+                <param name="input_primers" value="ipcress_test_input.txt" ftype="txt" />
+                <param name="input_seqs" value="targets.fasta" ftype="fasta" />
+                <output name="pcr_products" file="ipcress.out" />
+        </test>
+        </tests>
+        <help>
+ipcress is the In-silico PCR Experiment Simulation System.
+
+This is a tool for simulation of PCR experiments. You supply a file containing primers and a set of sequences, and it predicts PCR products.
+
+INPUT FORMAT
+
+The input for ipcress is a simple white-space delimited file describing
+one experiment per line.  Each line contains the following 5 fields:
+
+id                An identifier for this experiment
+primer_A          Sequence for the first primer
+primer_B          Sequence for the second primer
+min_product_len   Minimum product length to report
+max_product_len   Maximum product length to report
+
+Here is an example line in this format:
+
+ID0001 CATGCATGCATGC CGATGCANGCATGCT 900 1100
+
+MANUAL
+
+https://www.ebi.ac.uk/~guy/exonerate/ipcress.man.html
+
+        </help>
+</tool>
diff -r be070a68521e -r b321e0517be3 ipcress_gff.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ipcress_gff.xml	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,22 @@
+<?xml version="1.0"?>
+<tool id="ipcress_gff" name="IPCRESS to GFF">
+        <description>Convert output from In-Silico PCR Experiment Simulation System to GFF format</description>
+        <command>
+                awk '/^ipcress:/, split($2,HIT,":"){print HIT[1],$3,$4,$5,$6,$7,$8,$9,$10,$11}' $input1 | awk -v OFS='\t' '{print $1,"ipcress","PCR_product",$5,$8,".","+",".","Name="$2}' > $output1
+        </command>
+        <inputs>
+                <param format="txt" name="input1" type="data" label="iPCRESS ouptut" />
+        </inputs>
+        <outputs>
+                <data format="gff" name="output1" />
+        </outputs>
+        <tests>
+        <test>
+                <param name="input1" value="ipcress.out" ftype="txt" />
+                <output name="output1" file="ipcress_gff.out" />
+        </test>
+        </tests>
+        <help>
+Uses awk to parse IPCRESS output to gff file format
+        </help>
+</tool>
diff -r be070a68521e -r b321e0517be3 parse_primersearch.pl
--- a/parse_primersearch.pl	Thu Oct 18 19:47:07 2012 -0400
+++ b/parse_primersearch.pl	Thu May 22 20:30:19 2014 -0400
@@ -1,7 +1,7 @@
 #!/usr/bin/perl
 #parse_primersearch.pl
 #reformat EMBOSS primersearch output into columnar Galaxy interval format 
-
+#usage  perl parse_primersearch.pl <input primersearch file> <tabular output file>
 #Copyright 2012 John McCallum 
 #New Zealand Institute for Plant and Food Research
 #This program is free software: you can redistribute it and/or modify
@@ -20,7 +20,7 @@
 open (IN, "<$ARGV[0]");
 open (OUT, ">$ARGV[1]");
 
-#print OUT  "primerset_id","\t","sequence_id","\t","hit_start","\","mismatches","\t","amplimer_size",\n";
+
 
 
 
diff -r be070a68521e -r b321e0517be3 run_p3.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/run_p3.py	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,49 @@
+#!/usr/bin/pyrthon
+##run primer3 by passing Python dictionary
+
+#un_P3.py
+
+import subprocess as sp
+import copy
+
+
+if "check_output" not in dir(sp): # duck punch it in!
+    def f(*popenargs, **kwargs):
+        if 'stdout' in kwargs:
+            raise ValueError('stdout argument not allowed, it will be overridden.')
+        process = sp.Popen(stdout=sp.PIPE, *popenargs, **kwargs)
+        output, unused_err = process.communicate()
+        retcode = process.poll()
+        if retcode:
+            cmd = kwargs.get("args")
+            if cmd is None:
+                cmd = popenargs[0]
+            raise sp.CalledProcessError(retcode,cmd)
+        return output
+    sp.check_output = f
+
+
+
+
+##call P3 with dict of args, returns dict, no exception handling 
+def run_P3(target_dict):
+    p3_str=''
+    for key in target_dict:
+        p3_str+=key
+        p3_str+='='
+        p3_str+=str(target_dict[key])
+        p3_str+='\n'
+    p3_str+='='
+    input_str='echo -e \"' + p3_str + '\" | primer3_core '
+###exception handling to be added here
+    output = sp.check_output(input_str,shell=True)
+    output_fields=output.split('\n')
+    ##put output into a dict, omitting trailing =
+    P3_dict=dict([X.split('=') for X in output_fields][:len(output_fields)-2])
+    ##return iterable list
+    primer_list=[dict(PRIMER_RIGHT_SEQUENCE=P3_dict.get('PRIMER_RIGHT_'+ str(X) + '_SEQUENCE'),PRIMER_LEFT=P3_dict.get('PRIMER_LEFT_'+ str(X) ),PRIMER_RIGHT=P3_dict.get('PRIMER_RIGHT_'+ str(X) ),PRIMER_LEFT_SEQUENCE=P3_dict.get('PRIMER_LEFT_'+ str(X) + '_SEQUENCE')) for X in range(0,int(P3_dict.get('PRIMER_RIGHT_NUM_RETURNED'))-1)]
+    return(primer_list)
+
+
+
+
diff -r be070a68521e -r b321e0517be3 test-data/find_caps_output.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_caps_output.txt	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,1 @@
+k69_93535	1147	1149	k69_93535:SAMTOOLS:SNP:1147	TaqI	variant
diff -r be070a68521e -r b321e0517be3 test-data/freebayes_out.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/freebayes_out.vcf	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,500 @@
+##fileformat=VCFv4.1
+##fileDate=20140410
+##source=freeBayes version 0.9.6
+##reference=localref.fa
+##phasing=none
+##commandline="freebayes --bam localbam_0.bam --fasta-reference localref.fa --vcf /data/galaxy/galaxy-dist/database/files/000/dataset_31.dat"
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observations">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations">
+##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
+##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio.  Ratio between depth in samples with each called alternate allele and those without.">
+##INFO=<ID=XRM,Number=1,Type=Float,Description="Reference allele read mismatch rate: The rate of SNPs + MNPs + INDELs in reads supporting the reference allele.">
+##INFO=<ID=XRS,Number=1,Type=Float,Description="Reference allele read SNP rate: The rate of per-base mismatches (SNPs + MNPs) in reads supporting the reference allele.">
+##INFO=<ID=XRI,Number=1,Type=Float,Description="Reference allele read INDEL rate: The rate of INDELs (gaps) in reads supporting the reference allele.">
+##INFO=<ID=XAM,Number=A,Type=Float,Description="Alternate allele read mismatch rate: The rate of SNPs + MNPs + INDELs in reads supporting the alternate allele, excluding the called variant.">
+##INFO=<ID=XAS,Number=A,Type=Float,Description="Alternate allele read SNP rate: The rate of per-base mismatches (SNPs + MNPs) in reads supporting the alternate allele, excluding the called variant.">
+##INFO=<ID=XAI,Number=A,Type=Float,Description="Alternate allele read INDEL rate: The rate of INDELs (gaps) in reads supporting the alternate allele, excluding the called variant.">
+##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
+##INFO=<ID=BVAR,Number=0,Type=Flag,Description="The best genotype combination in the posterior is variant (non homozygous).">
+##INFO=<ID=CpG,Number=0,Type=Flag,Description="CpG site (either CpG, TpG or CpA)">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
+##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
+##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
+##INFO=<ID=HWE,Number=1,Type=Float,Description="Phred-scaled discrete HWE prior probability of the genotyping across all samples.">
+##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
+##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
+##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
+##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
+##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=GLE,Number=1,Type=String,Description="Genotype Likelihood Explicit, same as GL, but with tags to indicate the specific genotype.  For instance, 0^-75.22|1^-223.42|0/0^-323.03|1/0^-99.29|1/1^-802.53 represents both haploid and diploid genotype likilehoods in a biallelic context">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	unknown
+Chr1	106	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	200	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	217	.	G	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	249	.	T	A	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.02;XRS=0.02;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	586	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	669	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	682	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	1007	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0309278;XAS=0.0206186;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	1012	.	TGT	AGA	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0309278;XAS=0.0309278;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	1056	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0309278;XAS=0.0206186;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	1067	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0309278;XAS=0.0206186;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	1257	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	1305	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	1319	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	1330	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	1441	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0421053;XAS=0.0315789;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	1451	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0421053;XAS=0.0315789;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	1460	.	CTCTG	ATCTC	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0421053;XAS=0.0421053;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	1480	.	G	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0421053;XAS=0.0315789;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	1525	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0421053;XAS=0.0315789;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	1670	.	G	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	1673	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	1700	.	GC	TG	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=2X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=mnp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.02;XRS=0.02;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	1711	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	2117	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	2154	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	2485	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0103093;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	2490	.	AAA	CAC	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0103093;XAS=0.0103093;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	2906	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	2925	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	3371	.	CCCTT	GCCTA	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0105263;XAS=0.0105263;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	3389	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0105263;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	3431	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	3464	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	3746	.	C	CT	46.0861	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1M1I;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=ins;XAI=0;XAM=0.0204082;XAS=0.0204082;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:17.0704:1:0:0:1:46:-4.6,-0.30103,0
+Chr1	3766	.	C	A	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0102041;XAM=0.0204082;XAS=0.0102041;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	3790	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0102041;XAM=0.0204082;XAS=0.0102041;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	3855	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	5718	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	5754	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	5782	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	5792	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	6194	.	G	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	6212	.	G	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	6265	.	G	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	6482	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	6515	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	6520	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	6534	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	6602	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	6853	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	7015	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	7406	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	7422	.	G	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	7452	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	7460	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	7476	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	7843	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	7906	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	8214	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	8262	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	8279	.	G	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.04;XRS=0.04;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	8285	.	C	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.04;XRS=0.04;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	8288	.	G	C	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.04;XRS=0.04;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	8298	.	G	C	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.04;XRS=0.04;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	8305	.	G	C	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.04;XRS=0.04;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	8329	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	8509	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	8547	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	8633	.	G	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	8657	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	8894	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	8958	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	8968	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	9070	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	9100	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	9488	.	G	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	9514	.	GTTT	CTTG	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X2M1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=4;MEANALT=1;MQM=42;MQMR=34;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=complex;XAI=0;XAM=0.0208333;XAS=0.0208333;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	9532	.	A	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=34;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	10064	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	10072	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	10082	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	10099	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	10499	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	11126	.	C	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	11134	.	A	C	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	11141	.	C	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	11159	.	C	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	11169	.	A	C	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=6;MQMR=40;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.04;XRS=0.04;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	11208	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=6;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	11418	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	11547	.	A	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	11567	.	C	A	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.02;XRS=0.02;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	11582	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	13312	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	13336	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	13352	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	13652	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	13666	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	13728	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.02;XRS=0.02;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	14087	.	ATGAAA	GTGAGC	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X3M2X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=6;MEANALT=1;MQM=0;MQMR=18;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=1;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=complex;XAI=0.0365854;XAM=0.097561;XAS=0.0609756;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	14103	.	AGT	GGC	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X1M1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=3;MEANALT=1;MQM=0;MQMR=18;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=1;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=complex;XAI=0.0365854;XAM=0.097561;XAS=0.0609756;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	14119	.	A	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=18;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=1;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0487805;XAM=0.097561;XAS=0.0487805;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	14126	.	A	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=18;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=1;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0487805;XAM=0.097561;XAS=0.0487805;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	14131	.	GGAGTG	TGGGTT	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X1M1X2M1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=6;MEANALT=1;MQM=0;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=1;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=complex;XAI=0.0365854;XAM=0.097561;XAS=0.0609756;XRI=0;XRM=0.025;XRS=0.025	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	14141	.	TCA	CCC	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X1M1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=3;MEANALT=1;MQM=0;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=1;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=complex;XAI=0.0365854;XAM=0.097561;XAS=0.0609756;XRI=0;XRM=0.025;XRS=0.025	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	14159	.	G	A	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=1;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0487805;XAM=0.097561;XAS=0.0487805;XRI=0;XRM=0.025;XRS=0.025	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	14165	.	T	G	7.01833	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=2;MQM=18;MQMR=0;NS=1;NUMALT=1;ODDS=0;PAIRED=0;PAIREDR=1;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0.0487805;XRM=0.109756;XRS=0.0609756;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:0.628068:3:1:17:1:17:-3.23,-2.00103,-3.23
+Chr1	14167	.	A	T	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=1;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0487805;XAM=0.097561;XAS=0.0487805;XRI=0;XRM=0.025;XRS=0.025	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	14182	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=1;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0487805;XAM=0.097561;XAS=0.0487805;XRI=0;XRM=0.04;XRS=0.04;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	14201	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	14210	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	14230	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0222222;XAM=0.133333;XAS=0.111111;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	14240	.	C	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0222222;XAM=0.133333;XAS=0.111111;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	14247	.	G	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0222222;XAM=0.133333;XAS=0.111111;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	14256	.	A	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0222222;XAM=0.133333;XAS=0.111111;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	14262	.	TT	CC	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0.0222222;XAM=0.122222;XAS=0.1;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	14292	.	TCTG	CCTA	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X2M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=4;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0.0111111;XAM=0.133333;XAS=0.122222;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	14306	.	AC	TT	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0.0222222;XAM=0.122222;XAS=0.1;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	14312	.	CG	TA	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0.0222222;XAM=0.122222;XAS=0.1;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	14320	.	TCTTT	TCCCTA	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1M1I1M1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0.0111111;XAM=0.133333;XAS=0.122222;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	14327	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0222222;XAM=0.133333;XAS=0.111111;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	14595	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	14624	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	14629	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	14724	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	15170	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	15183	.	T	A	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.0103093;XRM=0.0206186;XRS=0.0103093;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	15199	.	CAA	AAT	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0103093;XAS=0.0103093;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	15209	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0103093;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	15599	.	TGG	GGC	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0103093;XAS=0.0103093;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	15624	.	A	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=40;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0103093;XAM=0.0103093;XAS=0;XRI=0;XRM=0.04;XRS=0.04;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	15625	.	A	C	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0.0103093;XRM=0.0206186;XRS=0.0103093;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	15670	.	C	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0.0103093;XRM=0.0206186;XRS=0.0103093;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	15685	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	15696	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	15981	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0315789;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	16021	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0315789;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	16050	.	CTGGG	ATGGC	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0315789;XAS=0.0315789;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	16059	.	A	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0105263;XAM=0.0315789;XAS=0.0210526;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	16085	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	16287	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	16502	.	GCA	CCT	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0.0108696;XAM=0.0217391;XAS=0.0108696;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	16512	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0217391;XAM=0.0217391;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	16519	.	TGTGT	GGTGG	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0.0108696;XAM=0.0217391;XAS=0.0108696;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	17672	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	17738	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	17849	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	17873	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	17878	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	18083	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	18090	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	18099	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	18205	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	18275	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	18285	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	18320	.	G	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	18370	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	18416	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	20586	.	G	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=27;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	20604	.	T	A	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=27;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	20625	.	G	T	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=13.5;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.01;XRS=0.01	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	20692	.	A	C	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	20702	.	T	A	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	20720	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	20891	.	G	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	20922	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	20967	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	20998	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	21007	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	21042	.	C	A	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=21;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.04;XRS=0.04;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	21055	.	G	A	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=21;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	21080	.	C	A	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=21;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	21165	.	T	A	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0104167;XAM=0.0104167;XAS=0;XRI=0;XRM=0.02;XRS=0.02;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	21189	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=25;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.0104167;XRM=0.0208333;XRS=0.0104167;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	21202	.	ACCT	CCCA,TCCT	20.1741	.	AB=0.5,0.5;ABP=3.0103,3.0103;AC=1,1;AF=0.5,0.5;AN=2;AO=1,1;CIGAR=1X2M1X,1X3M;DP=2;DPRA=0,0;EPP=5.18177,5.18177;EPPR=0;HWE=-0;LEN=4,1;MEANALT=2,2;MQM=25,42;MQMR=0;NS=1;NUMALT=2;ODDS=0.00237165;PAIRED=0,0;PAIREDR=0;RO=0;RPP=5.18177,5.18177;RPPR=0;RUN=1,1;SAP=5.18177,5.18177;SRP=0;TYPE=complex,snp;XAI=0,0;XAM=0.0104167,0.02;XAS=0.0104167,0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/2:1.71537:2:0:0:1,1:17,17:-3.23,-2.00103,-1.7,-2.00103,-0.30103,-1.7
+Chr1	21322	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	21342	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	21359	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	21584	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	21615	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	21821	.	G	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=21;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	21936	.	TGT	AGA	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=21;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0103093;XAS=0.0103093;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	21955	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=21;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0103093;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	22337	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	22345	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	22415	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0104167;XAM=0.0104167;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	22429	.	ATTG	CTTT	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X2M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=4;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0104167;XAS=0.0104167;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	22520	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	22539	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	22742	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	22801	.	G	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	22888	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	22919	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	23346	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	23360	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	23390	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	23432	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	23687	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	23716	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	23745	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	23812	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	23829	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	23959	.	TC	AG	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0.0104167;XAM=0.0104167;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	23989	.	ATCT	CTCA	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X2M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=4;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0208333;XAS=0.0208333;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	24095	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=26;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	24350	.	G	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	24377	.	G	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	24395	.	A	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0.0104167;XRM=0.03125;XRS=0.0208333;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	24413	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0.0104167;XRM=0.03125;XRS=0.0208333;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	24416	.	GAGT	TAGA	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X2M1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=4;MEANALT=1;MQM=0;MQMR=40;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=complex;XAI=0;XAM=0.0208333;XAS=0.0208333;XRI=0;XRM=0.04;XRS=0.04;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	24467	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	24477	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	24846	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	24889	.	A	C	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	24923	.	T	A	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	24964	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	25174	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	25301	.	A	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	25320	.	G	C	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	25345	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	25355	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	25550	.	A	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	25580	.	A	T	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=20;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.015625;XRS=0.0104167	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	25584	.	C	G	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=12.5;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0.01;XRS=0.01	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	25626	.	GCAC	TCAG	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X2M1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=4;MEANALT=1;MQM=40;MQMR=33.5;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=complex;XAI=0;XAM=0.0208333;XAS=0.0208333;XRI=0.00526316;XRM=0.0205263;XRS=0.0152632	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	25644	.	A	C	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=34.5;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0.00526316;XRM=0.0155263;XRS=0.0102632	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	25687	.	A	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=27;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0105263;XAM=0.0105263;XAS=0;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	25696	.	ACTCA	GCTCT,GCTCA	20.1741	.	AB=0.5,0.5;ABP=3.0103,3.0103;AC=1,1;AF=0.5,0.5;AN=2;AO=1,1;CIGAR=1X3M1X,1X4M;DP=2;DPRA=0,0;EPP=5.18177,5.18177;EPPR=0;HWE=-0;LEN=5,1;MEANALT=2,2;MQM=42,27;MQMR=0;NS=1;NUMALT=2;ODDS=0.00237165;PAIRED=0,0;PAIREDR=0;RO=0;RPP=5.18177,5.18177;RPPR=0;RUN=1,1;SAP=5.18177,5.18177;SRP=0;TYPE=complex,snp;XAI=0,0;XAM=0.0105263,0.01;XAS=0.0105263,0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/2:1.71537:2:0:0:1,1:17,17:-3.23,-2.00103,-1.7,-2.00103,-0.30103,-1.7
+Chr1	25944	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	25972	.	G	C	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	25981	.	G	T	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=21;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.025;XRS=0.025	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	25983	.	AA	TT	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=2X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=mnp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.015;XRS=0.015	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	26001	.	G	C	1.76687	.	AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=3.73412;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=9.52472;RUN=1;SAP=5.18177;SRP=3.73412;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.01;XRS=0.01	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76
+Chr1	26364	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	26420	.	G	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	27175	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	27431	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	27472	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	27556	.	A	AT	46.0861	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1M1I;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=ins;XAI=0;XAM=0.0102041;XAS=0.0102041;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:17.0704:1:0:0:1:46:-4.6,-0.30103,0
+Chr1	27610	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0102041;XAM=0.0102041;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	27909	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	28614	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	28993	.	TGGG	GGGC	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X2M1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=4;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=complex;XAI=0;XAM=0.0208333;XAS=0.0208333;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	29022	.	T	A	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.015625;XRS=0.0104167	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	29026	.	T	G	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0.01;XRS=0.01	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	29032	.	T	G	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0.01;XRS=0.01	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	29080	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	29218	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	29342	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	29463	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	29516	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	29528	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	29575	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	29580	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	30681	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0210526;XAS=0.0105263;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	30735	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0210526;XAS=0.0105263;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	30766	.	CTATT	GTATA	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0210526;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	31019	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	31054	.	G	C	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	31101	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	31400	.	GT	CG	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	31422	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	32027	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	32060	.	C	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	32166	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	32226	.	AA	CC	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	32480	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	32491	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	32651	.	A	C	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	32934	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	33054	.	G	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	33109	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	33143	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	33245	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	33274	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	33377	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	33392	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	33417	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	33713	.	C	A	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	33746	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	35247	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	35679	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	36145	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	36591	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	37260	.	AT	CA	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	37270	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	37283	.	G	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.04;XRS=0.04;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	37284	.	G	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.03;XRS=0.03;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	37295	.	A	C	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.04;XRS=0.04;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	37321	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	37610	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	37673	.	G	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	38268	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	38656	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	39013	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	39023	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	39460	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	39480	.	GA	TC	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=2X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=mnp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.03;XRS=0.03;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	39501	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	39508	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	41835	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	41885	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	42284	.	AGTTT	TGTTG	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	42628	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0222222;XAM=0.0222222;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	42637	.	ATTCC	CTTCG	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0.0111111;XAM=0.0222222;XAS=0.0111111;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	42652	.	TTTGT	ATTGA	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0.0111111;XAM=0.0222222;XAS=0.0111111;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	43145	.	GG	CC	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	43164	.	G	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	43173	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	43219	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	43437	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	44980	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	45144	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	45166	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	45311	.	G	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	45333	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	45385	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	45419	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	45427	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	45663	.	C	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	45685	.	AG	CT	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=2X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=mnp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	46052	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	46117	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	46251	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	46261	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	47385	.	G	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	47414	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	48446	.	T	A	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	48526	.	C	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	48789	.	T	A	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	48796	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=6;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	48811	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=6;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	48831	.	A	C	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	48838	.	A	C	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	48852	.	A	T	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=3;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.025;XRS=0.025	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	48907	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	48936	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	49044	.	G	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	49059	.	A	C	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=18;MQMR=20;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.0310417;XRS=0.0258333	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	49086	.	T	G	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0104167;XAM=0.0416667;XAS=0.03125;XRI=0;XRM=0.015;XRS=0.015	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	49088	.	C	G	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=18;MQMR=20;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.0310417;XRS=0.0258333	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	49091	.	T	G	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0104167;XAM=0.0416667;XAS=0.03125;XRI=0;XRM=0.015;XRS=0.015	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	49099	.	T	G	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0104167;XAM=0.0416667;XAS=0.03125;XRI=0;XRM=0.015;XRS=0.015	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	49124	.	AAAC	TAAA	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X2M1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=4;MEANALT=1;MQM=40;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=complex;XAI=0;XAM=0.0416667;XAS=0.0416667;XRI=0;XRM=0.015;XRS=0.015	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	49134	.	C	A	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0104167;XAM=0.0416667;XAS=0.03125;XRI=0;XRM=0.015;XRS=0.015	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	49493	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0315789;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	49543	.	TGCAA	GGCAT	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0315789;XAS=0.0315789;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	49553	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0315789;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	49583	.	G	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0315789;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	50222	.	ACAAAGA	CCCACTC	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X1M3X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=7;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	50557	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.02;XRS=0.02;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	50574	.	G	C	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	50603	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	50790	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	50828	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	50843	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	50958	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	51330	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=35;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	51606	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	51681	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	51984	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	51996	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	52061	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	53145	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	53423	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	53442	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	54071	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	54472	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	54525	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	54562	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	55358	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	55372	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	55415	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	55460	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	55491	.	AA	CC	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	55917	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	56372	.	G	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	56383	.	G	T	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=41;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.02;XRS=0.02	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	56399	.	A	C	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	56430	.	A	C	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	56448	.	C	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	56477	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	56586	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0102041;XAM=0.0204082;XAS=0.0102041;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	56642	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0102041;XAM=0.0204082;XAS=0.0102041;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	56672	.	T	TA	46.0861	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1M1I;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=ins;XAI=0;XAM=0.0204082;XAS=0.0204082;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:17.0704:1:0:0:1:46:-4.6,-0.30103,0
+Chr1	56708	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	56728	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	56743	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	56750	.	G	C	1.76687	.	AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=3.73412;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=28;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=3.73412;RUN=1;SAP=5.18177;SRP=3.73412;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76
+Chr1	56756	.	A	T	1.76687	.	AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=3.73412;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=28;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=3.73412;RUN=1;SAP=5.18177;SRP=3.73412;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76
+Chr1	56769	.	A	T	1.76687	.	AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=3.73412;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=28;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=9.52472;RUN=1;SAP=5.18177;SRP=3.73412;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.0266667;XRS=0.0266667	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76
+Chr1	56792	.	A	T	1.76687	.	AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=3.73412;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=28;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=9.52472;RUN=1;SAP=5.18177;SRP=3.73412;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76
+Chr1	56800	.	A	T	1.76687	.	AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=3.73412;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=28;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=9.52472;RUN=1;SAP=5.18177;SRP=3.73412;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76
+Chr1	56803	.	C	G	1.76687	.	AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=9.52472;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=28;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=9.52472;RUN=1;SAP=5.18177;SRP=9.52472;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76
+Chr1	56822	.	A	T	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=21;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.02;XRS=0.02	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	57075	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	57129	.	A	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	57130	.	A	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	57164	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	57166	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	57533	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0210526;XAS=0.0105263;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	57543	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0210526;XAS=0.0105263;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	57561	.	TTCGA	ATCGC	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0210526;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	57885	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	57929	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	58372	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	58383	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	58391	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	58399	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	58807	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	58825	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	58844	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	58862	.	A	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.03;XRS=0.03;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	59508	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0102041;XAM=0.0306122;XAS=0.0204082;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	59524	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0102041;XAM=0.0306122;XAS=0.0204082;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	59546	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0102041;XAM=0.0306122;XAS=0.0204082;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	59554	.	C	CG	46.0861	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1M1I;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=ins;XAI=0;XAM=0.0306122;XAS=0.0306122;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:17.0704:1:0:0:1:46:-4.6,-0.30103,0
+Chr1	61378	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	61387	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	61599	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	61652	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	61882	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0309278;XAS=0.0206186;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	61904	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0309278;XAS=0.0206186;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	61913	.	AGG	TGC	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0309278;XAS=0.0309278;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	61957	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0309278;XAS=0.0206186;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	62010	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	62056	.	T	A	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	62168	.	CCGCC	GCGCG	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	62290	.	T	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	62446	.	C	G	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=42;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.0152083;XRS=0.01	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	62447	.	CTAG	ATAC	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X2M1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=4;MEANALT=1;MQM=42;MQMR=21;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=complex;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.02;XRS=0.02	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	62462	.	C	G	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=42;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.0152083;XRS=0.01	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	62478	.	C	G	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=21;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.0152083;XRS=0.01	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	62514	.	G	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.02;XRS=0.02;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	62598	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	62634	.	T	G	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.04;XRS=0.04;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	62658	.	T	G	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=21;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.01;XRS=0.01	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	62665	.	G	C	2.50735	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=21;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.01;XRS=0.01	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
+Chr1	62686	.	A	T	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	62697	.	C	A	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
+Chr1	62758	.	G	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	62769	.	A	C	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	62841	.	T	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	62852	.	C	G	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	62929	.	C	A	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=18;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	63049	.	A	T	17.1701	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
+Chr1	63120	.	C	A	4.77465	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=18;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR	GT:GQ:DP:RO:QR:AO:QA:GL	0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
diff -r be070a68521e -r b321e0517be3 test-data/freebayes_vcf_to_gff_output.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/freebayes_vcf_to_gff_output.gff	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,449 @@
+#gff-version 3
+Chr1	SAMTOOLS	SNP	106	106	17.1701	.	.	ID=Chr1:SNP:106;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	200	200	17.1701	.	.	ID=Chr1:SNP:200;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	217	217	4.77465	.	.	ID=Chr1:SNP:217;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	249	249	4.77465	.	.	ID=Chr1:SNP:249;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	586	586	17.1701	.	.	ID=Chr1:SNP:586;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	669	669	4.77465	.	.	ID=Chr1:SNP:669;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	682	682	4.77465	.	.	ID=Chr1:SNP:682;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	1007	1007	17.1701	.	.	ID=Chr1:SNP:1007;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1012	1012	17.1701	.	.	ID=Chr1:SNP:1012;Variant_seq=AGA;Reference_seq=TGT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1056	1056	17.1701	.	.	ID=Chr1:SNP:1056;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1067	1067	17.1701	.	.	ID=Chr1:SNP:1067;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1257	1257	17.1701	.	.	ID=Chr1:SNP:1257;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1305	1305	17.1701	.	.	ID=Chr1:SNP:1305;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1319	1319	17.1701	.	.	ID=Chr1:SNP:1319;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1330	1330	17.1701	.	.	ID=Chr1:SNP:1330;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1441	1441	17.1701	.	.	ID=Chr1:SNP:1441;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1451	1451	17.1701	.	.	ID=Chr1:SNP:1451;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1460	1460	17.1701	.	.	ID=Chr1:SNP:1460;Variant_seq=ATCTC;Reference_seq=CTCTG;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1480	1480	17.1701	.	.	ID=Chr1:SNP:1480;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1525	1525	17.1701	.	.	ID=Chr1:SNP:1525;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1670	1670	4.77465	.	.	ID=Chr1:SNP:1670;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	1673	1673	4.77465	.	.	ID=Chr1:SNP:1673;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	1700	1700	4.77465	.	.	ID=Chr1:SNP:1700;Variant_seq=TG;Reference_seq=GC;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	1711	1711	4.77465	.	.	ID=Chr1:SNP:1711;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	2117	2117	17.1701	.	.	ID=Chr1:SNP:2117;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	2154	2154	17.1701	.	.	ID=Chr1:SNP:2154;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	2485	2485	17.1701	.	.	ID=Chr1:SNP:2485;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	2490	2490	17.1701	.	.	ID=Chr1:SNP:2490;Variant_seq=CAC;Reference_seq=AAA;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	2906	2906	17.1701	.	.	ID=Chr1:SNP:2906;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	2925	2925	17.1701	.	.	ID=Chr1:SNP:2925;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	3371	3371	17.1701	.	.	ID=Chr1:SNP:3371;Variant_seq=GCCTA;Reference_seq=CCCTT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	3389	3389	17.1701	.	.	ID=Chr1:SNP:3389;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	3431	3431	17.1701	.	.	ID=Chr1:SNP:3431;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	3464	3464	17.1701	.	.	ID=Chr1:SNP:3464;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	3746	3746	46.0861	.	.	ID=Chr1:SNP:3746;Variant_seq=CT;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	3766	3766	4.77465	.	.	ID=Chr1:SNP:3766;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	3790	3790	4.77465	.	.	ID=Chr1:SNP:3790;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	3855	3855	17.1701	.	.	ID=Chr1:SNP:3855;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	5718	5718	17.1701	.	.	ID=Chr1:SNP:5718;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	5754	5754	17.1701	.	.	ID=Chr1:SNP:5754;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	5782	5782	17.1701	.	.	ID=Chr1:SNP:5782;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	5792	5792	17.1701	.	.	ID=Chr1:SNP:5792;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	6194	6194	17.1701	.	.	ID=Chr1:SNP:6194;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	6212	6212	17.1701	.	.	ID=Chr1:SNP:6212;Variant_seq=A;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	6265	6265	17.1701	.	.	ID=Chr1:SNP:6265;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	6482	6482	17.1701	.	.	ID=Chr1:SNP:6482;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	6515	6515	17.1701	.	.	ID=Chr1:SNP:6515;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	6520	6520	17.1701	.	.	ID=Chr1:SNP:6520;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	6534	6534	17.1701	.	.	ID=Chr1:SNP:6534;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	6602	6602	17.1701	.	.	ID=Chr1:SNP:6602;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	6853	6853	17.1701	.	.	ID=Chr1:SNP:6853;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	7015	7015	17.1701	.	.	ID=Chr1:SNP:7015;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	7406	7406	17.1701	.	.	ID=Chr1:SNP:7406;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	7422	7422	17.1701	.	.	ID=Chr1:SNP:7422;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	7452	7452	17.1701	.	.	ID=Chr1:SNP:7452;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	7460	7460	17.1701	.	.	ID=Chr1:SNP:7460;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	7476	7476	17.1701	.	.	ID=Chr1:SNP:7476;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	7843	7843	17.1701	.	.	ID=Chr1:SNP:7843;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	7906	7906	17.1701	.	.	ID=Chr1:SNP:7906;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	8214	8214	17.1701	.	.	ID=Chr1:SNP:8214;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	8262	8262	17.1701	.	.	ID=Chr1:SNP:8262;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	8279	8279	4.77465	.	.	ID=Chr1:SNP:8279;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	8285	8285	4.77465	.	.	ID=Chr1:SNP:8285;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	8288	8288	4.77465	.	.	ID=Chr1:SNP:8288;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	8298	8298	4.77465	.	.	ID=Chr1:SNP:8298;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	8305	8305	4.77465	.	.	ID=Chr1:SNP:8305;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	8329	8329	17.1701	.	.	ID=Chr1:SNP:8329;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	8509	8509	17.1701	.	.	ID=Chr1:SNP:8509;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	8547	8547	17.1701	.	.	ID=Chr1:SNP:8547;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	8633	8633	17.1701	.	.	ID=Chr1:SNP:8633;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	8657	8657	17.1701	.	.	ID=Chr1:SNP:8657;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	8894	8894	17.1701	.	.	ID=Chr1:SNP:8894;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	8958	8958	17.1701	.	.	ID=Chr1:SNP:8958;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	8968	8968	17.1701	.	.	ID=Chr1:SNP:8968;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	9070	9070	17.1701	.	.	ID=Chr1:SNP:9070;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	9100	9100	17.1701	.	.	ID=Chr1:SNP:9100;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	9488	9488	17.1701	.	.	ID=Chr1:SNP:9488;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	9514	9514	4.77465	.	.	ID=Chr1:SNP:9514;Variant_seq=CTTG;Reference_seq=GTTT;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	9532	9532	4.77465	.	.	ID=Chr1:SNP:9532;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	10064	10064	17.1701	.	.	ID=Chr1:SNP:10064;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	10072	10072	17.1701	.	.	ID=Chr1:SNP:10072;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	10082	10082	17.1701	.	.	ID=Chr1:SNP:10082;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	10099	10099	17.1701	.	.	ID=Chr1:SNP:10099;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	10499	10499	17.1701	.	.	ID=Chr1:SNP:10499;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	11126	11126	4.77465	.	.	ID=Chr1:SNP:11126;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	11134	11134	4.77465	.	.	ID=Chr1:SNP:11134;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	11141	11141	4.77465	.	.	ID=Chr1:SNP:11141;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	11159	11159	4.77465	.	.	ID=Chr1:SNP:11159;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	11169	11169	4.77465	.	.	ID=Chr1:SNP:11169;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	11208	11208	17.1701	.	.	ID=Chr1:SNP:11208;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	11418	11418	17.1701	.	.	ID=Chr1:SNP:11418;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	11547	11547	4.77465	.	.	ID=Chr1:SNP:11547;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	11567	11567	4.77465	.	.	ID=Chr1:SNP:11567;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	11582	11582	17.1701	.	.	ID=Chr1:SNP:11582;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	13312	13312	17.1701	.	.	ID=Chr1:SNP:13312;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	13336	13336	17.1701	.	.	ID=Chr1:SNP:13336;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	13352	13352	17.1701	.	.	ID=Chr1:SNP:13352;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	13652	13652	17.1701	.	.	ID=Chr1:SNP:13652;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	13666	13666	17.1701	.	.	ID=Chr1:SNP:13666;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	13728	13728	4.77465	.	.	ID=Chr1:SNP:13728;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	14087	14087	4.77465	.	.	ID=Chr1:SNP:14087;Variant_seq=GTGAGC;Reference_seq=ATGAAA;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	14103	14103	4.77465	.	.	ID=Chr1:SNP:14103;Variant_seq=GGC;Reference_seq=AGT;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	14119	14119	4.77465	.	.	ID=Chr1:SNP:14119;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	14126	14126	4.77465	.	.	ID=Chr1:SNP:14126;Variant_seq=G;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	14131	14131	2.50735	.	.	ID=Chr1:SNP:14131;Variant_seq=TGGGTT;Reference_seq=GGAGTG;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	14141	14141	2.50735	.	.	ID=Chr1:SNP:14141;Variant_seq=CCC;Reference_seq=TCA;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	14159	14159	2.50735	.	.	ID=Chr1:SNP:14159;Variant_seq=A;Reference_seq=G;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	14165	14165	7.01833	.	.	ID=Chr1:SNP:14165;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HOM_mut 
+Chr1	SAMTOOLS	SNP	14167	14167	2.50735	.	.	ID=Chr1:SNP:14167;Variant_seq=T;Reference_seq=A;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	14182	14182	4.77465	.	.	ID=Chr1:SNP:14182;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	14201	14201	17.1701	.	.	ID=Chr1:SNP:14201;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14210	14210	17.1701	.	.	ID=Chr1:SNP:14210;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14230	14230	17.1701	.	.	ID=Chr1:SNP:14230;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14240	14240	17.1701	.	.	ID=Chr1:SNP:14240;Variant_seq=T;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14247	14247	17.1701	.	.	ID=Chr1:SNP:14247;Variant_seq=A;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14256	14256	17.1701	.	.	ID=Chr1:SNP:14256;Variant_seq=G;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14262	14262	17.1701	.	.	ID=Chr1:SNP:14262;Variant_seq=CC;Reference_seq=TT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14292	14292	17.1701	.	.	ID=Chr1:SNP:14292;Variant_seq=CCTA;Reference_seq=TCTG;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14306	14306	17.1701	.	.	ID=Chr1:SNP:14306;Variant_seq=TT;Reference_seq=AC;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14312	14312	17.1701	.	.	ID=Chr1:SNP:14312;Variant_seq=TA;Reference_seq=CG;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14320	14320	17.1701	.	.	ID=Chr1:SNP:14320;Variant_seq=TCCCTA;Reference_seq=TCTTT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14327	14327	17.1701	.	.	ID=Chr1:SNP:14327;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14595	14595	17.1701	.	.	ID=Chr1:SNP:14595;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14624	14624	17.1701	.	.	ID=Chr1:SNP:14624;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14629	14629	17.1701	.	.	ID=Chr1:SNP:14629;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14724	14724	17.1701	.	.	ID=Chr1:SNP:14724;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	15170	15170	17.1701	.	.	ID=Chr1:SNP:15170;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	15183	15183	4.77465	.	.	ID=Chr1:SNP:15183;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	15199	15199	17.1701	.	.	ID=Chr1:SNP:15199;Variant_seq=AAT;Reference_seq=CAA;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	15209	15209	17.1701	.	.	ID=Chr1:SNP:15209;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	15599	15599	17.1701	.	.	ID=Chr1:SNP:15599;Variant_seq=GGC;Reference_seq=TGG;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	15624	15624	4.77465	.	.	ID=Chr1:SNP:15624;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	15625	15625	4.77465	.	.	ID=Chr1:SNP:15625;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	15670	15670	4.77465	.	.	ID=Chr1:SNP:15670;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	15685	15685	17.1701	.	.	ID=Chr1:SNP:15685;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	15696	15696	17.1701	.	.	ID=Chr1:SNP:15696;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	15981	15981	17.1701	.	.	ID=Chr1:SNP:15981;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	16021	16021	17.1701	.	.	ID=Chr1:SNP:16021;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	16050	16050	17.1701	.	.	ID=Chr1:SNP:16050;Variant_seq=ATGGC;Reference_seq=CTGGG;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	16059	16059	4.77465	.	.	ID=Chr1:SNP:16059;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	16085	16085	17.1701	.	.	ID=Chr1:SNP:16085;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	16287	16287	17.1701	.	.	ID=Chr1:SNP:16287;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	16502	16502	17.1701	.	.	ID=Chr1:SNP:16502;Variant_seq=CCT;Reference_seq=GCA;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	16512	16512	17.1701	.	.	ID=Chr1:SNP:16512;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	16519	16519	17.1701	.	.	ID=Chr1:SNP:16519;Variant_seq=GGTGG;Reference_seq=TGTGT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	17672	17672	17.1701	.	.	ID=Chr1:SNP:17672;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	17738	17738	17.1701	.	.	ID=Chr1:SNP:17738;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	17849	17849	17.1701	.	.	ID=Chr1:SNP:17849;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	17873	17873	17.1701	.	.	ID=Chr1:SNP:17873;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	17878	17878	17.1701	.	.	ID=Chr1:SNP:17878;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	18083	18083	17.1701	.	.	ID=Chr1:SNP:18083;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	18090	18090	17.1701	.	.	ID=Chr1:SNP:18090;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	18099	18099	17.1701	.	.	ID=Chr1:SNP:18099;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	18205	18205	17.1701	.	.	ID=Chr1:SNP:18205;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	18275	18275	17.1701	.	.	ID=Chr1:SNP:18275;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	18285	18285	17.1701	.	.	ID=Chr1:SNP:18285;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	18320	18320	17.1701	.	.	ID=Chr1:SNP:18320;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	18370	18370	17.1701	.	.	ID=Chr1:SNP:18370;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	18416	18416	17.1701	.	.	ID=Chr1:SNP:18416;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	20586	20586	4.77465	.	.	ID=Chr1:SNP:20586;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	20604	20604	4.77465	.	.	ID=Chr1:SNP:20604;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	20625	20625	2.50735	.	.	ID=Chr1:SNP:20625;Variant_seq=T;Reference_seq=G;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	20692	20692	4.77465	.	.	ID=Chr1:SNP:20692;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	20702	20702	4.77465	.	.	ID=Chr1:SNP:20702;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	20720	20720	17.1701	.	.	ID=Chr1:SNP:20720;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	20891	20891	17.1701	.	.	ID=Chr1:SNP:20891;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	20922	20922	17.1701	.	.	ID=Chr1:SNP:20922;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	20967	20967	17.1701	.	.	ID=Chr1:SNP:20967;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	20998	20998	17.1701	.	.	ID=Chr1:SNP:20998;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	21007	21007	17.1701	.	.	ID=Chr1:SNP:21007;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	21042	21042	4.77465	.	.	ID=Chr1:SNP:21042;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	21055	21055	4.77465	.	.	ID=Chr1:SNP:21055;Variant_seq=A;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	21080	21080	4.77465	.	.	ID=Chr1:SNP:21080;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	21165	21165	4.77465	.	.	ID=Chr1:SNP:21165;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	21189	21189	4.77465	.	.	ID=Chr1:SNP:21189;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	21202	21202	20.1741	.	.	ID=Chr1:SNP:21202;Variant_seq=CCCA,TCCT;Reference_seq=ACCT;Total_reads=2;Zygosity=2:NA 
+Chr1	SAMTOOLS	SNP	21322	21322	17.1701	.	.	ID=Chr1:SNP:21322;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	21342	21342	17.1701	.	.	ID=Chr1:SNP:21342;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	21359	21359	17.1701	.	.	ID=Chr1:SNP:21359;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	21584	21584	17.1701	.	.	ID=Chr1:SNP:21584;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	21615	21615	17.1701	.	.	ID=Chr1:SNP:21615;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	21821	21821	17.1701	.	.	ID=Chr1:SNP:21821;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	21936	21936	17.1701	.	.	ID=Chr1:SNP:21936;Variant_seq=AGA;Reference_seq=TGT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	21955	21955	17.1701	.	.	ID=Chr1:SNP:21955;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	22337	22337	17.1701	.	.	ID=Chr1:SNP:22337;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	22345	22345	17.1701	.	.	ID=Chr1:SNP:22345;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	22415	22415	17.1701	.	.	ID=Chr1:SNP:22415;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	22429	22429	17.1701	.	.	ID=Chr1:SNP:22429;Variant_seq=CTTT;Reference_seq=ATTG;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	22520	22520	17.1701	.	.	ID=Chr1:SNP:22520;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	22539	22539	17.1701	.	.	ID=Chr1:SNP:22539;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	22742	22742	17.1701	.	.	ID=Chr1:SNP:22742;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	22801	22801	17.1701	.	.	ID=Chr1:SNP:22801;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	22888	22888	17.1701	.	.	ID=Chr1:SNP:22888;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	22919	22919	17.1701	.	.	ID=Chr1:SNP:22919;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23346	23346	17.1701	.	.	ID=Chr1:SNP:23346;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23360	23360	17.1701	.	.	ID=Chr1:SNP:23360;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23390	23390	17.1701	.	.	ID=Chr1:SNP:23390;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23432	23432	17.1701	.	.	ID=Chr1:SNP:23432;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23687	23687	17.1701	.	.	ID=Chr1:SNP:23687;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23716	23716	17.1701	.	.	ID=Chr1:SNP:23716;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23745	23745	17.1701	.	.	ID=Chr1:SNP:23745;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23812	23812	17.1701	.	.	ID=Chr1:SNP:23812;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23829	23829	17.1701	.	.	ID=Chr1:SNP:23829;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23959	23959	17.1701	.	.	ID=Chr1:SNP:23959;Variant_seq=AG;Reference_seq=TC;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23989	23989	17.1701	.	.	ID=Chr1:SNP:23989;Variant_seq=CTCA;Reference_seq=ATCT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	24095	24095	17.1701	.	.	ID=Chr1:SNP:24095;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	24350	24350	17.1701	.	.	ID=Chr1:SNP:24350;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	24377	24377	17.1701	.	.	ID=Chr1:SNP:24377;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	24395	24395	4.77465	.	.	ID=Chr1:SNP:24395;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	24413	24413	4.77465	.	.	ID=Chr1:SNP:24413;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	24416	24416	4.77465	.	.	ID=Chr1:SNP:24416;Variant_seq=TAGA;Reference_seq=GAGT;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	24467	24467	17.1701	.	.	ID=Chr1:SNP:24467;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	24477	24477	17.1701	.	.	ID=Chr1:SNP:24477;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	24846	24846	17.1701	.	.	ID=Chr1:SNP:24846;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	24889	24889	4.77465	.	.	ID=Chr1:SNP:24889;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	24923	24923	4.77465	.	.	ID=Chr1:SNP:24923;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	24964	24964	17.1701	.	.	ID=Chr1:SNP:24964;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	25174	25174	17.1701	.	.	ID=Chr1:SNP:25174;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	25301	25301	4.77465	.	.	ID=Chr1:SNP:25301;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	25320	25320	4.77465	.	.	ID=Chr1:SNP:25320;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	25345	25345	4.77465	.	.	ID=Chr1:SNP:25345;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	25355	25355	17.1701	.	.	ID=Chr1:SNP:25355;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	25550	25550	4.77465	.	.	ID=Chr1:SNP:25550;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	25580	25580	2.50735	.	.	ID=Chr1:SNP:25580;Variant_seq=T;Reference_seq=A;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	25584	25584	2.50735	.	.	ID=Chr1:SNP:25584;Variant_seq=G;Reference_seq=C;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	25626	25626	2.50735	.	.	ID=Chr1:SNP:25626;Variant_seq=TCAG;Reference_seq=GCAC;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	25644	25644	2.50735	.	.	ID=Chr1:SNP:25644;Variant_seq=C;Reference_seq=A;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	25687	25687	4.77465	.	.	ID=Chr1:SNP:25687;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	25696	25696	20.1741	.	.	ID=Chr1:SNP:25696;Variant_seq=GCTCT,GCTCA;Reference_seq=ACTCA;Total_reads=2;Zygosity=2:NA 
+Chr1	SAMTOOLS	SNP	25944	25944	17.1701	.	.	ID=Chr1:SNP:25944;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	25972	25972	4.77465	.	.	ID=Chr1:SNP:25972;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	25981	25981	2.50735	.	.	ID=Chr1:SNP:25981;Variant_seq=T;Reference_seq=G;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	25983	25983	2.50735	.	.	ID=Chr1:SNP:25983;Variant_seq=TT;Reference_seq=AA;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	26001	26001	1.76687	.	.	ID=Chr1:SNP:26001;Variant_seq=C;Reference_seq=G;Total_reads=4;Zygosity=4:HET 
+Chr1	SAMTOOLS	SNP	26364	26364	17.1701	.	.	ID=Chr1:SNP:26364;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	26420	26420	17.1701	.	.	ID=Chr1:SNP:26420;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	27175	27175	17.1701	.	.	ID=Chr1:SNP:27175;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	27431	27431	17.1701	.	.	ID=Chr1:SNP:27431;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	27472	27472	17.1701	.	.	ID=Chr1:SNP:27472;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	27556	27556	46.0861	.	.	ID=Chr1:SNP:27556;Variant_seq=AT;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	27610	27610	17.1701	.	.	ID=Chr1:SNP:27610;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	27909	27909	17.1701	.	.	ID=Chr1:SNP:27909;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	28614	28614	17.1701	.	.	ID=Chr1:SNP:28614;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	28993	28993	4.77465	.	.	ID=Chr1:SNP:28993;Variant_seq=GGGC;Reference_seq=TGGG;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	29022	29022	2.50735	.	.	ID=Chr1:SNP:29022;Variant_seq=A;Reference_seq=T;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	29026	29026	2.50735	.	.	ID=Chr1:SNP:29026;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	29032	29032	2.50735	.	.	ID=Chr1:SNP:29032;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	29080	29080	17.1701	.	.	ID=Chr1:SNP:29080;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	29218	29218	17.1701	.	.	ID=Chr1:SNP:29218;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	29342	29342	17.1701	.	.	ID=Chr1:SNP:29342;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	29463	29463	17.1701	.	.	ID=Chr1:SNP:29463;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	29516	29516	4.77465	.	.	ID=Chr1:SNP:29516;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	29528	29528	4.77465	.	.	ID=Chr1:SNP:29528;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	29575	29575	17.1701	.	.	ID=Chr1:SNP:29575;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	29580	29580	17.1701	.	.	ID=Chr1:SNP:29580;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	30681	30681	17.1701	.	.	ID=Chr1:SNP:30681;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	30735	30735	17.1701	.	.	ID=Chr1:SNP:30735;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	30766	30766	17.1701	.	.	ID=Chr1:SNP:30766;Variant_seq=GTATA;Reference_seq=CTATT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	31019	31019	17.1701	.	.	ID=Chr1:SNP:31019;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	31054	31054	4.77465	.	.	ID=Chr1:SNP:31054;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	31101	31101	17.1701	.	.	ID=Chr1:SNP:31101;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	31400	31400	17.1701	.	.	ID=Chr1:SNP:31400;Variant_seq=CG;Reference_seq=GT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	31422	31422	17.1701	.	.	ID=Chr1:SNP:31422;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	32027	32027	17.1701	.	.	ID=Chr1:SNP:32027;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	32060	32060	17.1701	.	.	ID=Chr1:SNP:32060;Variant_seq=T;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	32166	32166	17.1701	.	.	ID=Chr1:SNP:32166;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	32226	32226	17.1701	.	.	ID=Chr1:SNP:32226;Variant_seq=CC;Reference_seq=AA;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	32480	32480	17.1701	.	.	ID=Chr1:SNP:32480;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	32491	32491	17.1701	.	.	ID=Chr1:SNP:32491;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	32651	32651	4.77465	.	.	ID=Chr1:SNP:32651;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	32934	32934	17.1701	.	.	ID=Chr1:SNP:32934;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	33054	33054	17.1701	.	.	ID=Chr1:SNP:33054;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	33109	33109	17.1701	.	.	ID=Chr1:SNP:33109;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	33143	33143	17.1701	.	.	ID=Chr1:SNP:33143;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	33245	33245	17.1701	.	.	ID=Chr1:SNP:33245;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	33274	33274	17.1701	.	.	ID=Chr1:SNP:33274;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	33377	33377	17.1701	.	.	ID=Chr1:SNP:33377;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	33392	33392	17.1701	.	.	ID=Chr1:SNP:33392;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	33417	33417	17.1701	.	.	ID=Chr1:SNP:33417;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	33713	33713	4.77465	.	.	ID=Chr1:SNP:33713;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	33746	33746	17.1701	.	.	ID=Chr1:SNP:33746;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	35247	35247	17.1701	.	.	ID=Chr1:SNP:35247;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	35679	35679	17.1701	.	.	ID=Chr1:SNP:35679;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	36145	36145	17.1701	.	.	ID=Chr1:SNP:36145;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	36591	36591	17.1701	.	.	ID=Chr1:SNP:36591;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	37260	37260	17.1701	.	.	ID=Chr1:SNP:37260;Variant_seq=CA;Reference_seq=AT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	37270	37270	17.1701	.	.	ID=Chr1:SNP:37270;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	37283	37283	4.77465	.	.	ID=Chr1:SNP:37283;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	37284	37284	4.77465	.	.	ID=Chr1:SNP:37284;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	37295	37295	4.77465	.	.	ID=Chr1:SNP:37295;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	37321	37321	17.1701	.	.	ID=Chr1:SNP:37321;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	37610	37610	17.1701	.	.	ID=Chr1:SNP:37610;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	37673	37673	17.1701	.	.	ID=Chr1:SNP:37673;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	38268	38268	17.1701	.	.	ID=Chr1:SNP:38268;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	38656	38656	17.1701	.	.	ID=Chr1:SNP:38656;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	39013	39013	17.1701	.	.	ID=Chr1:SNP:39013;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	39023	39023	17.1701	.	.	ID=Chr1:SNP:39023;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	39460	39460	4.77465	.	.	ID=Chr1:SNP:39460;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	39480	39480	4.77465	.	.	ID=Chr1:SNP:39480;Variant_seq=TC;Reference_seq=GA;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	39501	39501	4.77465	.	.	ID=Chr1:SNP:39501;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	39508	39508	4.77465	.	.	ID=Chr1:SNP:39508;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	41835	41835	17.1701	.	.	ID=Chr1:SNP:41835;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	41885	41885	17.1701	.	.	ID=Chr1:SNP:41885;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	42284	42284	17.1701	.	.	ID=Chr1:SNP:42284;Variant_seq=TGTTG;Reference_seq=AGTTT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	42628	42628	17.1701	.	.	ID=Chr1:SNP:42628;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	42637	42637	17.1701	.	.	ID=Chr1:SNP:42637;Variant_seq=CTTCG;Reference_seq=ATTCC;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	42652	42652	17.1701	.	.	ID=Chr1:SNP:42652;Variant_seq=ATTGA;Reference_seq=TTTGT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	43145	43145	17.1701	.	.	ID=Chr1:SNP:43145;Variant_seq=CC;Reference_seq=GG;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	43164	43164	17.1701	.	.	ID=Chr1:SNP:43164;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	43173	43173	17.1701	.	.	ID=Chr1:SNP:43173;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	43219	43219	17.1701	.	.	ID=Chr1:SNP:43219;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	43437	43437	17.1701	.	.	ID=Chr1:SNP:43437;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	44980	44980	17.1701	.	.	ID=Chr1:SNP:44980;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	45144	45144	17.1701	.	.	ID=Chr1:SNP:45144;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	45166	45166	17.1701	.	.	ID=Chr1:SNP:45166;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	45311	45311	17.1701	.	.	ID=Chr1:SNP:45311;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	45333	45333	17.1701	.	.	ID=Chr1:SNP:45333;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	45385	45385	17.1701	.	.	ID=Chr1:SNP:45385;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	45419	45419	17.1701	.	.	ID=Chr1:SNP:45419;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	45427	45427	17.1701	.	.	ID=Chr1:SNP:45427;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	45663	45663	4.77465	.	.	ID=Chr1:SNP:45663;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	45685	45685	4.77465	.	.	ID=Chr1:SNP:45685;Variant_seq=CT;Reference_seq=AG;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	46052	46052	17.1701	.	.	ID=Chr1:SNP:46052;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	46117	46117	17.1701	.	.	ID=Chr1:SNP:46117;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	46251	46251	17.1701	.	.	ID=Chr1:SNP:46251;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	46261	46261	17.1701	.	.	ID=Chr1:SNP:46261;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	47385	47385	17.1701	.	.	ID=Chr1:SNP:47385;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	47414	47414	17.1701	.	.	ID=Chr1:SNP:47414;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	48446	48446	4.77465	.	.	ID=Chr1:SNP:48446;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	48526	48526	4.77465	.	.	ID=Chr1:SNP:48526;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	48789	48789	4.77465	.	.	ID=Chr1:SNP:48789;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	48796	48796	4.77465	.	.	ID=Chr1:SNP:48796;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	48811	48811	4.77465	.	.	ID=Chr1:SNP:48811;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	48831	48831	4.77465	.	.	ID=Chr1:SNP:48831;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	48838	48838	4.77465	.	.	ID=Chr1:SNP:48838;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	48852	48852	2.50735	.	.	ID=Chr1:SNP:48852;Variant_seq=T;Reference_seq=A;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	48907	48907	17.1701	.	.	ID=Chr1:SNP:48907;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	48936	48936	17.1701	.	.	ID=Chr1:SNP:48936;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	49044	49044	17.1701	.	.	ID=Chr1:SNP:49044;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	49059	49059	2.50735	.	.	ID=Chr1:SNP:49059;Variant_seq=C;Reference_seq=A;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	49086	49086	2.50735	.	.	ID=Chr1:SNP:49086;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	49088	49088	2.50735	.	.	ID=Chr1:SNP:49088;Variant_seq=G;Reference_seq=C;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	49091	49091	2.50735	.	.	ID=Chr1:SNP:49091;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	49099	49099	2.50735	.	.	ID=Chr1:SNP:49099;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	49124	49124	2.50735	.	.	ID=Chr1:SNP:49124;Variant_seq=TAAA;Reference_seq=AAAC;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	49134	49134	2.50735	.	.	ID=Chr1:SNP:49134;Variant_seq=A;Reference_seq=C;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	49493	49493	17.1701	.	.	ID=Chr1:SNP:49493;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	49543	49543	17.1701	.	.	ID=Chr1:SNP:49543;Variant_seq=GGCAT;Reference_seq=TGCAA;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	49553	49553	17.1701	.	.	ID=Chr1:SNP:49553;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	49583	49583	17.1701	.	.	ID=Chr1:SNP:49583;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	50222	50222	17.1701	.	.	ID=Chr1:SNP:50222;Variant_seq=CCCACTC;Reference_seq=ACAAAGA;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	50557	50557	4.77465	.	.	ID=Chr1:SNP:50557;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	50574	50574	4.77465	.	.	ID=Chr1:SNP:50574;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	50603	50603	17.1701	.	.	ID=Chr1:SNP:50603;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	50790	50790	17.1701	.	.	ID=Chr1:SNP:50790;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	50828	50828	17.1701	.	.	ID=Chr1:SNP:50828;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	50843	50843	17.1701	.	.	ID=Chr1:SNP:50843;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	50958	50958	17.1701	.	.	ID=Chr1:SNP:50958;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	51330	51330	4.77465	.	.	ID=Chr1:SNP:51330;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	51606	51606	17.1701	.	.	ID=Chr1:SNP:51606;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	51681	51681	17.1701	.	.	ID=Chr1:SNP:51681;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	51984	51984	17.1701	.	.	ID=Chr1:SNP:51984;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	51996	51996	17.1701	.	.	ID=Chr1:SNP:51996;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	52061	52061	17.1701	.	.	ID=Chr1:SNP:52061;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	53145	53145	17.1701	.	.	ID=Chr1:SNP:53145;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	53423	53423	17.1701	.	.	ID=Chr1:SNP:53423;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	53442	53442	17.1701	.	.	ID=Chr1:SNP:53442;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	54071	54071	17.1701	.	.	ID=Chr1:SNP:54071;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	54472	54472	17.1701	.	.	ID=Chr1:SNP:54472;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	54525	54525	17.1701	.	.	ID=Chr1:SNP:54525;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	54562	54562	17.1701	.	.	ID=Chr1:SNP:54562;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	55358	55358	17.1701	.	.	ID=Chr1:SNP:55358;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	55372	55372	17.1701	.	.	ID=Chr1:SNP:55372;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	55415	55415	17.1701	.	.	ID=Chr1:SNP:55415;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	55460	55460	17.1701	.	.	ID=Chr1:SNP:55460;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	55491	55491	17.1701	.	.	ID=Chr1:SNP:55491;Variant_seq=CC;Reference_seq=AA;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	55917	55917	17.1701	.	.	ID=Chr1:SNP:55917;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	56372	56372	4.77465	.	.	ID=Chr1:SNP:56372;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	56383	56383	2.50735	.	.	ID=Chr1:SNP:56383;Variant_seq=T;Reference_seq=G;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	56399	56399	4.77465	.	.	ID=Chr1:SNP:56399;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	56430	56430	4.77465	.	.	ID=Chr1:SNP:56430;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	56448	56448	4.77465	.	.	ID=Chr1:SNP:56448;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	56477	56477	17.1701	.	.	ID=Chr1:SNP:56477;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	56586	56586	17.1701	.	.	ID=Chr1:SNP:56586;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	56642	56642	17.1701	.	.	ID=Chr1:SNP:56642;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	56672	56672	46.0861	.	.	ID=Chr1:SNP:56672;Variant_seq=TA;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	56708	56708	17.1701	.	.	ID=Chr1:SNP:56708;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	56728	56728	17.1701	.	.	ID=Chr1:SNP:56728;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	56743	56743	17.1701	.	.	ID=Chr1:SNP:56743;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	56750	56750	1.76687	.	.	ID=Chr1:SNP:56750;Variant_seq=C;Reference_seq=G;Total_reads=4;Zygosity=4:HET 
+Chr1	SAMTOOLS	SNP	56756	56756	1.76687	.	.	ID=Chr1:SNP:56756;Variant_seq=T;Reference_seq=A;Total_reads=4;Zygosity=4:HET 
+Chr1	SAMTOOLS	SNP	56769	56769	1.76687	.	.	ID=Chr1:SNP:56769;Variant_seq=T;Reference_seq=A;Total_reads=4;Zygosity=4:HET 
+Chr1	SAMTOOLS	SNP	56792	56792	1.76687	.	.	ID=Chr1:SNP:56792;Variant_seq=T;Reference_seq=A;Total_reads=4;Zygosity=4:HET 
+Chr1	SAMTOOLS	SNP	56800	56800	1.76687	.	.	ID=Chr1:SNP:56800;Variant_seq=T;Reference_seq=A;Total_reads=4;Zygosity=4:HET 
+Chr1	SAMTOOLS	SNP	56803	56803	1.76687	.	.	ID=Chr1:SNP:56803;Variant_seq=G;Reference_seq=C;Total_reads=4;Zygosity=4:HET 
+Chr1	SAMTOOLS	SNP	56822	56822	2.50735	.	.	ID=Chr1:SNP:56822;Variant_seq=T;Reference_seq=A;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	57075	57075	4.77465	.	.	ID=Chr1:SNP:57075;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	57129	57129	4.77465	.	.	ID=Chr1:SNP:57129;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	57130	57130	4.77465	.	.	ID=Chr1:SNP:57130;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	57164	57164	17.1701	.	.	ID=Chr1:SNP:57164;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	57166	57166	17.1701	.	.	ID=Chr1:SNP:57166;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	57533	57533	17.1701	.	.	ID=Chr1:SNP:57533;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	57543	57543	17.1701	.	.	ID=Chr1:SNP:57543;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	57561	57561	17.1701	.	.	ID=Chr1:SNP:57561;Variant_seq=ATCGC;Reference_seq=TTCGA;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	57885	57885	17.1701	.	.	ID=Chr1:SNP:57885;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	57929	57929	17.1701	.	.	ID=Chr1:SNP:57929;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	58372	58372	17.1701	.	.	ID=Chr1:SNP:58372;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	58383	58383	17.1701	.	.	ID=Chr1:SNP:58383;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	58391	58391	17.1701	.	.	ID=Chr1:SNP:58391;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	58399	58399	17.1701	.	.	ID=Chr1:SNP:58399;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	58807	58807	17.1701	.	.	ID=Chr1:SNP:58807;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	58825	58825	17.1701	.	.	ID=Chr1:SNP:58825;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	58844	58844	17.1701	.	.	ID=Chr1:SNP:58844;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	58862	58862	4.77465	.	.	ID=Chr1:SNP:58862;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	59508	59508	17.1701	.	.	ID=Chr1:SNP:59508;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	59524	59524	17.1701	.	.	ID=Chr1:SNP:59524;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	59546	59546	17.1701	.	.	ID=Chr1:SNP:59546;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	59554	59554	46.0861	.	.	ID=Chr1:SNP:59554;Variant_seq=CG;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	61378	61378	17.1701	.	.	ID=Chr1:SNP:61378;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	61387	61387	17.1701	.	.	ID=Chr1:SNP:61387;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	61599	61599	17.1701	.	.	ID=Chr1:SNP:61599;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	61652	61652	17.1701	.	.	ID=Chr1:SNP:61652;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	61882	61882	17.1701	.	.	ID=Chr1:SNP:61882;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	61904	61904	17.1701	.	.	ID=Chr1:SNP:61904;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	61913	61913	17.1701	.	.	ID=Chr1:SNP:61913;Variant_seq=TGC;Reference_seq=AGG;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	61957	61957	17.1701	.	.	ID=Chr1:SNP:61957;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	62010	62010	17.1701	.	.	ID=Chr1:SNP:62010;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	62056	62056	4.77465	.	.	ID=Chr1:SNP:62056;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	62168	62168	17.1701	.	.	ID=Chr1:SNP:62168;Variant_seq=GCGCG;Reference_seq=CCGCC;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	62290	62290	17.1701	.	.	ID=Chr1:SNP:62290;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	62446	62446	2.50735	.	.	ID=Chr1:SNP:62446;Variant_seq=G;Reference_seq=C;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	62447	62447	2.50735	.	.	ID=Chr1:SNP:62447;Variant_seq=ATAC;Reference_seq=CTAG;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	62462	62462	2.50735	.	.	ID=Chr1:SNP:62462;Variant_seq=G;Reference_seq=C;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	62478	62478	2.50735	.	.	ID=Chr1:SNP:62478;Variant_seq=G;Reference_seq=C;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	62514	62514	4.77465	.	.	ID=Chr1:SNP:62514;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	62598	62598	17.1701	.	.	ID=Chr1:SNP:62598;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	62634	62634	4.77465	.	.	ID=Chr1:SNP:62634;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	62658	62658	2.50735	.	.	ID=Chr1:SNP:62658;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	62665	62665	2.50735	.	.	ID=Chr1:SNP:62665;Variant_seq=C;Reference_seq=G;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	62686	62686	4.77465	.	.	ID=Chr1:SNP:62686;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	62697	62697	4.77465	.	.	ID=Chr1:SNP:62697;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	62758	62758	17.1701	.	.	ID=Chr1:SNP:62758;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	62769	62769	17.1701	.	.	ID=Chr1:SNP:62769;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	62841	62841	17.1701	.	.	ID=Chr1:SNP:62841;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	62852	62852	17.1701	.	.	ID=Chr1:SNP:62852;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	62929	62929	17.1701	.	.	ID=Chr1:SNP:62929;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	63049	63049	17.1701	.	.	ID=Chr1:SNP:63049;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	63120	63120	4.77465	.	.	ID=Chr1:SNP:63120;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
diff -r be070a68521e -r b321e0517be3 test-data/ipcress.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ipcress.out	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,341 @@
+
+Ipcress result
+--------------
+ Experiment: k69_93535:SAMTOOLS:SNP:1147
+    Primers: A B
+     Target: k69_93535:filter(unmasked)
+    Matches: 20/20 23/23
+    Product: 83 bp (range 50-100)
+Result type: forward
+
+...GGACAGGGAAGCTTCATAGG................................. # forward
+   ||||||||||||||||||||-->
+5'-GGACAGGGAAGCTTCATAGG-3' 3'-CTCCTAAACTAGAAAGTCCAAAC-5' # primers
+                           <--|||||||||||||||||||||||
+..............................CTCCTAAACTAGAAAGTCCAAAC... # revcomp
+--
+ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1147 83 A 1088 0 B 1148 0 forward
+
+Ipcress result
+--------------
+ Experiment: k69_93535:SAMTOOLS:SNP:1147
+    Primers: A B
+     Target: k69_93535:filter(unmasked)
+    Matches: 21/21 21/21
+    Product: 86 bp (range 50-100)
+Result type: forward
+
+...CTTTGAGTCTGAACGCATTTG............................... # forward
+   |||||||||||||||||||||-->
+5'-CTTTGAGTCTGAACGCATTTG-3' 3'-CTTCTTTGCCCTCTACTTTGT-5' # primers
+                            <--|||||||||||||||||||||
+...............................CTTCTTTGCCCTCTACTTTGT... # revcomp
+--
+ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1147 86 A 1109 0 B 1174 0 forward
+
+Ipcress result
+--------------
+ Experiment: k69_93535:SAMTOOLS:SNP:1147
+    Primers: A B
+     Target: k69_93535:filter(unmasked)
+    Matches: 20/20 20/20
+    Product: 87 bp (range 50-100)
+Result type: forward
+
+...TTTGAGTCTGAACGCATTTG.............................. # forward
+   ||||||||||||||||||||-->
+5'-TTTGAGTCTGAACGCATTTG-3' 3'-CTTTGCCCTCTACTTTGTTC-5' # primers
+                           <--||||||||||||||||||||
+..............................CTTTGCCCTCTACTTTGTTC... # revcomp
+--
+ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1147 87 A 1110 0 B 1177 0 forward
+
+Ipcress result
+--------------
+ Experiment: k69_93535:SAMTOOLS:SNP:1147
+    Primers: A B
+     Target: k69_93535:filter(unmasked)
+    Matches: 21/21 21/21
+    Product: 89 bp (range 50-100)
+Result type: forward
+
+...CTTTGAGTCTGAACGCATTTG............................... # forward
+   |||||||||||||||||||||-->
+5'-CTTTGAGTCTGAACGCATTTG-3' 3'-CTTTGCCCTCTACTTTGTTCT-5' # primers
+                            <--|||||||||||||||||||||
+...............................CTTTGCCCTCTACTTTGTTCT... # revcomp
+--
+ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1147 89 A 1109 0 B 1177 0 forward
+
+Ipcress result
+--------------
+ Experiment: k69_93535:SAMTOOLS:SNP:1147
+    Primers: A B
+     Target: k69_93535:filter(unmasked)
+    Matches: 21/21 21/21
+    Product: 93 bp (range 50-100)
+Result type: forward
+
+...CTTTGAGTCTGAACGCATTTG............................... # forward
+   |||||||||||||||||||||-->
+5'-CTTTGAGTCTGAACGCATTTG-3' 3'-GCCCTCTACTTTGTTCTAAAC-5' # primers
+                            <--|||||||||||||||||||||
+...............................GCCCTCTACTTTGTTCTAAAC... # revcomp
+--
+ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1147 93 A 1109 0 B 1181 0 forward
+
+Ipcress result
+--------------
+ Experiment: k69_93535:SAMTOOLS:SNP:1336
+    Primers: A B
+     Target: k69_93535:filter(unmasked)
+    Matches: 20/20 22/22
+    Product: 82 bp (range 50-100)
+Result type: forward
+
+...TTAGAAGGAACGCGAGAAGG................................ # forward
+   ||||||||||||||||||||-->
+5'-TTAGAAGGAACGCGAGAAGG-3' 3'-GAATGCGGATCAAACCAACAAC-5' # primers
+                           <--||||||||||||||||||||||
+..............................GAATGCGGATCAAACCAACAAC... # revcomp
+--
+ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1336 82 A 1297 0 B 1357 0 forward
+
+Ipcress result
+--------------
+ Experiment: k69_93535:SAMTOOLS:SNP:1336
+    Primers: A B
+     Target: k69_93535:filter(unmasked)
+    Matches: 20/20 20/20
+    Product: 85 bp (range 50-100)
+Result type: forward
+
+...TTTAGAAGGAACGCGAGAAG.............................. # forward
+   ||||||||||||||||||||-->
+5'-TTTAGAAGGAACGCGAGAAG-3' 3'-GCGGATCAAACCAACAACAA-5' # primers
+                           <--||||||||||||||||||||
+..............................GCGGATCAAACCAACAACAA... # revcomp
+--
+ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1336 85 A 1296 0 B 1361 0 forward
+
+Ipcress result
+--------------
+ Experiment: k69_93535:SAMTOOLS:SNP:1336
+    Primers: A B
+     Target: k69_93535:filter(unmasked)
+    Matches: 21/21 20/20
+    Product: 86 bp (range 50-100)
+Result type: forward
+
+...GTTTAGAAGGAACGCGAGAAG.............................. # forward
+   |||||||||||||||||||||-->
+5'-GTTTAGAAGGAACGCGAGAAG-3' 3'-GCGGATCAAACCAACAACAA-5' # primers
+                            <--||||||||||||||||||||
+...............................GCGGATCAAACCAACAACAA... # revcomp
+--
+ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1336 86 A 1295 0 B 1361 0 forward
+
+Ipcress result
+--------------
+ Experiment: k69_93535:SAMTOOLS:SNP:1336
+    Primers: A B
+     Target: k69_93535:filter(unmasked)
+    Matches: 20/20 22/22
+    Product: 87 bp (range 50-100)
+Result type: forward
+
+...TTAGAAGGAACGCGAGAAGG................................ # forward
+   ||||||||||||||||||||-->
+5'-TTAGAAGGAACGCGAGAAGG-3' 3'-CGGATCAAACCAACAACAACTC-5' # primers
+                           <--||||||||||||||||||||||
+..............................CGGATCAAACCAACAACAACTC... # revcomp
+--
+ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1336 87 A 1297 0 B 1362 0 forward
+
+Ipcress result
+--------------
+ Experiment: k69_93535:SAMTOOLS:SNP:1336
+    Primers: A B
+     Target: k69_93535:filter(unmasked)
+    Matches: 20/20 22/22
+    Product: 88 bp (range 50-100)
+Result type: forward
+
+...TTAGAAGGAACGCGAGAAGG................................ # forward
+   ||||||||||||||||||||-->
+5'-TTAGAAGGAACGCGAGAAGG-3' 3'-GGATCAAACCAACAACAACTCG-5' # primers
+                           <--||||||||||||||||||||||
+..............................GGATCAAACCAACAACAACTCG... # revcomp
+--
+ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1336 88 A 1297 0 B 1363 0 forward
+
+Ipcress result
+--------------
+ Experiment: k69_98089:SAMTOOLS:SNP:30
+    Primers: A B
+     Target: k69_98089:filter(unmasked)
+    Matches: 25/25 19/19
+    Product: 88 bp (range 50-100)
+Result type: forward
+
+...CAAATCCAAACATGTTATCTTCTTC............................. # forward
+   |||||||||||||||||||||||||-->
+5'-CAAATCCAAACATGTTATCTTCTTC-3' 3'-GCGAGTTGCAGTCTAGTAG-5' # primers
+                                <--|||||||||||||||||||
+...................................GCGAGTTGCAGTCTAGTAG... # revcomp
+--
+ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:30 88 A 1 0 B 70 0 forward
+
+Ipcress result
+--------------
+ Experiment: k69_98089:SAMTOOLS:SNP:30
+    Primers: A B
+     Target: k69_98089:filter(unmasked)
+    Matches: 25/25 20/20
+    Product: 90 bp (range 50-100)
+Result type: forward
+
+...CAAATCCAAACATGTTATCTTCTTC.............................. # forward
+   |||||||||||||||||||||||||-->
+5'-CAAATCCAAACATGTTATCTTCTTC-3' 3'-CGAGTTGCAGTCTAGTAGTT-5' # primers
+                                <--||||||||||||||||||||
+...................................CGAGTTGCAGTCTAGTAGTT... # revcomp
+--
+ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:30 90 A 1 0 B 71 0 forward
+
+Ipcress result
+--------------
+ Experiment: k69_98089:SAMTOOLS:SNP:30
+    Primers: A B
+     Target: k69_98089:filter(unmasked)
+    Matches: 25/25 21/21
+    Product: 91 bp (range 50-100)
+Result type: forward
+
+...CAAATCCAAACATGTTATCTTCTTC............................... # forward
+   |||||||||||||||||||||||||-->
+5'-CAAATCCAAACATGTTATCTTCTTC-3' 3'-CGAGTTGCAGTCTAGTAGTTG-5' # primers
+                                <--|||||||||||||||||||||
+...................................CGAGTTGCAGTCTAGTAGTTG... # revcomp
+--
+ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:30 91 A 1 0 B 71 0 forward
+
+Ipcress result
+--------------
+ Experiment: k69_98089:SAMTOOLS:SNP:30
+    Primers: A B
+     Target: k69_98089:filter(unmasked)
+    Matches: 25/25 20/20
+    Product: 96 bp (range 50-100)
+Result type: forward
+
+...CAAATCCAAACATGTTATCTTCTTC.............................. # forward
+   |||||||||||||||||||||||||-->
+5'-CAAATCCAAACATGTTATCTTCTTC-3' 3'-GCAGTCTAGTAGTTGTGCTT-5' # primers
+                                <--||||||||||||||||||||
+...................................GCAGTCTAGTAGTTGTGCTT... # revcomp
+--
+ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:30 96 A 1 0 B 77 0 forward
+
+Ipcress result
+--------------
+ Experiment: k69_98089:SAMTOOLS:SNP:30
+    Primers: A B
+     Target: k69_98089:filter(unmasked)
+    Matches: 25/25 21/21
+    Product: 97 bp (range 50-100)
+Result type: forward
+
+...CAAATCCAAACATGTTATCTTCTTC............................... # forward
+   |||||||||||||||||||||||||-->
+5'-CAAATCCAAACATGTTATCTTCTTC-3' 3'-GCAGTCTAGTAGTTGTGCTTG-5' # primers
+                                <--|||||||||||||||||||||
+...................................GCAGTCTAGTAGTTGTGCTTG... # revcomp
+--
+ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:30 97 A 1 0 B 77 0 forward
+
+Ipcress result
+--------------
+ Experiment: k69_98089:SAMTOOLS:SNP:550
+    Primers: A B
+     Target: k69_98089:filter(unmasked)
+    Matches: 22/22 24/24
+    Product: 88 bp (range 50-100)
+Result type: forward
+
+...TGAATTGATACTGAAATTCGGG.................................. # forward
+   ||||||||||||||||||||||-->
+5'-TGAATTGATACTGAAATTCGGG-3' 3'-CTAACACCTTTGAAAGTACATACG-5' # primers
+                             <--||||||||||||||||||||||||
+................................CTAACACCTTTGAAAGTACATACG... # revcomp
+--
+ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:550 88 A 499 0 B 563 0 forward
+
+Ipcress result
+--------------
+ Experiment: k69_98089:SAMTOOLS:SNP:550
+    Primers: A B
+     Target: k69_98089:filter(unmasked)
+    Matches: 22/22 24/24
+    Product: 77 bp (range 50-100)
+Result type: forward
+
+...TGAAATTCGGGAAGACTGAAAG.................................. # forward
+   ||||||||||||||||||||||-->
+5'-TGAAATTCGGGAAGACTGAAAG-3' 3'-CTAACACCTTTGAAAGTACATACG-5' # primers
+                             <--||||||||||||||||||||||||
+................................CTAACACCTTTGAAAGTACATACG... # revcomp
+--
+ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:550 77 A 510 0 B 563 0 forward
+
+Ipcress result
+--------------
+ Experiment: k69_98089:SAMTOOLS:SNP:550
+    Primers: A B
+     Target: k69_98089:filter(unmasked)
+    Matches: 19/19 25/25
+    Product: 75 bp (range 50-100)
+Result type: forward
+
+...CGGGAAGACTGAAAGAACG................................... # forward
+   |||||||||||||||||||-->
+5'-CGGGAAGACTGAAAGAACG-3' 3'-CACCTTTGAAAGTACATACGATAGA-5' # primers
+                          <--|||||||||||||||||||||||||
+.............................CACCTTTGAAAGTACATACGATAGA... # revcomp
+--
+ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:550 75 A 517 0 B 567 0 forward
+
+Ipcress result
+--------------
+ Experiment: k69_98089:SAMTOOLS:SNP:550
+    Primers: A B
+     Target: k69_98089:filter(unmasked)
+    Matches: 21/21 25/25
+    Product: 81 bp (range 50-100)
+Result type: forward
+
+...GAAATTCGGGAAGACTGAAAG................................... # forward
+   |||||||||||||||||||||-->
+5'-GAAATTCGGGAAGACTGAAAG-3' 3'-CACCTTTGAAAGTACATACGATAGA-5' # primers
+                            <--|||||||||||||||||||||||||
+...............................CACCTTTGAAAGTACATACGATAGA... # revcomp
+--
+ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:550 81 A 511 0 B 567 0 forward
+
+Ipcress result
+--------------
+ Experiment: k69_98089:SAMTOOLS:SNP:550
+    Primers: A B
+     Target: k69_98089:filter(unmasked)
+    Matches: 22/22 25/25
+    Product: 79 bp (range 50-100)
+Result type: forward
+
+...AATTCGGGAAGACTGAAAGAAC................................... # forward
+   ||||||||||||||||||||||-->
+5'-AATTCGGGAAGACTGAAAGAAC-3' 3'-CACCTTTGAAAGTACATACGATAGA-5' # primers
+                             <--|||||||||||||||||||||||||
+................................CACCTTTGAAAGTACATACGATAGA... # revcomp
+--
+ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:550 79 A 513 0 B 567 0 forward
+-- completed ipcress analysis
diff -r be070a68521e -r b321e0517be3 test-data/ipcress_gff.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ipcress_gff.out	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,20 @@
+k69_93535	ipcress	PCR_product	1088	1148	.	+	.	Name=k69_93535:SAMTOOLS:SNP:1147
+k69_93535	ipcress	PCR_product	1109	1174	.	+	.	Name=k69_93535:SAMTOOLS:SNP:1147
+k69_93535	ipcress	PCR_product	1110	1177	.	+	.	Name=k69_93535:SAMTOOLS:SNP:1147
+k69_93535	ipcress	PCR_product	1109	1177	.	+	.	Name=k69_93535:SAMTOOLS:SNP:1147
+k69_93535	ipcress	PCR_product	1109	1181	.	+	.	Name=k69_93535:SAMTOOLS:SNP:1147
+k69_93535	ipcress	PCR_product	1297	1357	.	+	.	Name=k69_93535:SAMTOOLS:SNP:1336
+k69_93535	ipcress	PCR_product	1296	1361	.	+	.	Name=k69_93535:SAMTOOLS:SNP:1336
+k69_93535	ipcress	PCR_product	1295	1361	.	+	.	Name=k69_93535:SAMTOOLS:SNP:1336
+k69_93535	ipcress	PCR_product	1297	1362	.	+	.	Name=k69_93535:SAMTOOLS:SNP:1336
+k69_93535	ipcress	PCR_product	1297	1363	.	+	.	Name=k69_93535:SAMTOOLS:SNP:1336
+k69_98089	ipcress	PCR_product	1	70	.	+	.	Name=k69_98089:SAMTOOLS:SNP:30
+k69_98089	ipcress	PCR_product	1	71	.	+	.	Name=k69_98089:SAMTOOLS:SNP:30
+k69_98089	ipcress	PCR_product	1	71	.	+	.	Name=k69_98089:SAMTOOLS:SNP:30
+k69_98089	ipcress	PCR_product	1	77	.	+	.	Name=k69_98089:SAMTOOLS:SNP:30
+k69_98089	ipcress	PCR_product	1	77	.	+	.	Name=k69_98089:SAMTOOLS:SNP:30
+k69_98089	ipcress	PCR_product	499	563	.	+	.	Name=k69_98089:SAMTOOLS:SNP:550
+k69_98089	ipcress	PCR_product	510	563	.	+	.	Name=k69_98089:SAMTOOLS:SNP:550
+k69_98089	ipcress	PCR_product	517	567	.	+	.	Name=k69_98089:SAMTOOLS:SNP:550
+k69_98089	ipcress	PCR_product	511	567	.	+	.	Name=k69_98089:SAMTOOLS:SNP:550
+k69_98089	ipcress	PCR_product	513	567	.	+	.	Name=k69_98089:SAMTOOLS:SNP:550
diff -r be070a68521e -r b321e0517be3 test-data/ipcress_test_input.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ipcress_test_input.txt	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,20 @@
+k69_93535:SAMTOOLS:SNP:1147 CTTTGAGTCTGAACGCATTTG TGTTTCATCTCCCGTTTCTTC
+k69_93535:SAMTOOLS:SNP:1147 CTTTGAGTCTGAACGCATTTG TCTTGTTTCATCTCCCGTTTC
+k69_93535:SAMTOOLS:SNP:1147 CTTTGAGTCTGAACGCATTTG CAAATCTTGTTTCATCTCCCG
+k69_93535:SAMTOOLS:SNP:1147 TTTGAGTCTGAACGCATTTG CTTGTTTCATCTCCCGTTTC
+k69_93535:SAMTOOLS:SNP:1147 GGACAGGGAAGCTTCATAGG CAAACCTGAAAGATCAAATCCTC
+k69_93535:SAMTOOLS:SNP:1336 TTAGAAGGAACGCGAGAAGG CAACAACCAAACTAGGCGTAAG
+k69_93535:SAMTOOLS:SNP:1336 TTAGAAGGAACGCGAGAAGG CTCAACAACAACCAAACTAGGC
+k69_93535:SAMTOOLS:SNP:1336 TTAGAAGGAACGCGAGAAGG GCTCAACAACAACCAAACTAGG
+k69_93535:SAMTOOLS:SNP:1336 TTTAGAAGGAACGCGAGAAG AACAACAACCAAACTAGGCG
+k69_93535:SAMTOOLS:SNP:1336 GTTTAGAAGGAACGCGAGAAG AACAACAACCAAACTAGGCG
+k69_98089:SAMTOOLS:SNP:30 CAAATCCAAACATGTTATCTTCTTC TTCGTGTTGATGATCTGACG
+k69_98089:SAMTOOLS:SNP:30 CAAATCCAAACATGTTATCTTCTTC GTTCGTGTTGATGATCTGACG
+k69_98089:SAMTOOLS:SNP:30 CAAATCCAAACATGTTATCTTCTTC TTGATGATCTGACGTTGAGC
+k69_98089:SAMTOOLS:SNP:30 CAAATCCAAACATGTTATCTTCTTC GTTGATGATCTGACGTTGAGC
+k69_98089:SAMTOOLS:SNP:30 CAAATCCAAACATGTTATCTTCTTC GATGATCTGACGTTGAGCG
+k69_98089:SAMTOOLS:SNP:550 TGAATTGATACTGAAATTCGGG GCATACATGAAAGTTTCCACAATC
+k69_98089:SAMTOOLS:SNP:550 CGGGAAGACTGAAAGAACG AGATAGCATACATGAAAGTTTCCAC
+k69_98089:SAMTOOLS:SNP:550 GAAATTCGGGAAGACTGAAAG AGATAGCATACATGAAAGTTTCCAC
+k69_98089:SAMTOOLS:SNP:550 AATTCGGGAAGACTGAAAGAAC AGATAGCATACATGAAAGTTTCCAC
+k69_98089:SAMTOOLS:SNP:550 TGAAATTCGGGAAGACTGAAAG GCATACATGAAAGTTTCCACAATC
diff -r be070a68521e -r b321e0517be3 test-data/mpileup_out.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpileup_out.vcf	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,500 @@
+##fileformat=VCFv4.1
+##samtoolsVersion=0.1.19-44428cd
+##reference=file:///tmp/tmp-SAMTOOLS-zkHTpr/reference_input.fa
+##contig=<ID=Chr1,length=17971566>
+##contig=<ID=Chr10,length=15490421>
+##contig=<ID=Chr11,length=17082262>
+##contig=<ID=Chr12,length=13002763>
+##contig=<ID=Chr13,length=17372821>
+##contig=<ID=Chr14,length=12031045>
+##contig=<ID=Chr15,length=19001909>
+##contig=<ID=Chr16,length=11476499>
+##contig=<ID=Chr17,length=14675105>
+##contig=<ID=Chr18,length=14814751>
+##contig=<ID=Chr19,length=11145676>
+##contig=<ID=Chr2,length=15003700>
+##contig=<ID=Chr20,length=14375345>
+##contig=<ID=Chr21,length=14287830>
+##contig=<ID=Chr22,length=12982530>
+##contig=<ID=Chr23,length=20688064>
+##contig=<ID=Chr24,length=17702303>
+##contig=<ID=Chr25,length=14321294>
+##contig=<ID=Chr26,length=17153587>
+##contig=<ID=Chr27,length=10917718>
+##contig=<ID=Chr28,length=16406049>
+##contig=<ID=Chr29,length=14180785>
+##contig=<ID=Chr3,length=20519224>
+##contig=<ID=Chr4,length=13065296>
+##contig=<ID=Chr5,length=18825850>
+##contig=<ID=Chr6,length=18208465>
+##contig=<ID=Chr7,length=18704015>
+##contig=<ID=Chr8,length=21083321>
+##contig=<ID=Chr9,length=11598160>
+##contig=<ID=Unknow,length=177361715>
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
+##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
+##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
+##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=IS,Number=2,Type=Float,Description="Maximum number of reads supporting an indel and fraction of indel reads">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
+##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
+##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
+##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
+##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
+##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
+##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
+##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
+##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
+##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
+##INFO=<ID=QBD,Number=1,Type=Float,Description="Quality by Depth: QUAL/#reads">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Read Position Bias">
+##INFO=<ID=MDV,Number=1,Type=Integer,Description="Maximum number of high-quality nonRef reads in samples">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias (v2) for filtering splice-site artefacts in RNA-seq data. Note: this version may be broken.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality non-reference bases">
+##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	/tmp/tmp-SAMTOOLS-zkHTpr/bam_input_0.bam
+Chr1	14086	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14087	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	14088	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14089	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14090	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14091	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	14092	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	14093	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14094	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14095	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14096	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14097	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14098	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14099	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14100	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14101	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14102	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14103	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	14104	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14105	.	T	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	14106	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14107	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14108	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14109	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14110	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14111	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14112	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14113	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14114	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14115	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14116	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14117	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14118	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14119	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	14120	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14121	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14122	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14123	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14124	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14125	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14126	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	14127	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14128	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14129	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14130	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14131	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	14132	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14133	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	14134	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14135	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14136	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	14137	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14138	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14139	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14140	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14141	.	T	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	14142	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14143	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	14144	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14145	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14146	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14147	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14148	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14149	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14150	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14151	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14152	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14153	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14154	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14155	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14156	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14157	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14158	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14159	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	14160	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14161	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14162	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14163	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14164	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14165	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14166	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14167	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	14168	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14169	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14170	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14171	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14172	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14173	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14174	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14175	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14176	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14177	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14178	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14179	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14180	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14181	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14182	.	T	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	14183	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14184	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14185	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14230	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	14231	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14232	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14233	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14234	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14235	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14236	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14237	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14238	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14239	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14240	.	C	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	14241	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14242	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14243	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14244	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14245	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14246	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14247	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	14248	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14249	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14250	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14251	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14252	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14253	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14254	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14255	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14256	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	14257	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14258	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14259	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14260	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14261	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14262	.	T	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	14263	.	T	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	14264	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14265	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14266	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14267	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14268	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14269	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14270	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14271	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14272	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14273	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14274	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14275	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14276	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14277	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14278	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14279	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14280	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14281	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14282	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14283	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14284	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14285	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14286	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14287	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14288	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14289	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14290	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14291	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14292	.	T	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	14293	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14294	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14295	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	14296	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14297	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14298	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14299	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14300	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14301	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14302	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14303	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14304	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14305	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14306	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	14307	.	C	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	14308	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14309	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14310	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14311	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14312	.	C	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	14313	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	14314	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14315	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14316	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14317	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14318	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14319	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14320	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14320	.	TC	.	33.5	.	INDEL;IS=1,1.000000;DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-39	PL	4
+Chr1	14321	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14322	.	T	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	14323	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14324	.	T	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	14325	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14326	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	14327	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	14328	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120479	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120480	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120481	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120482	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120483	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120484	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120485	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120486	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120487	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120488	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120489	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120490	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120491	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120492	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120493	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120494	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120495	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120496	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120497	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120498	.	C	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	120499	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120500	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120501	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120502	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120503	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120504	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120505	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120506	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120507	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120508	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	120509	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120510	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120511	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120512	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120513	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120514	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120515	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	120516	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120517	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120518	.	C	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	120519	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120520	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120521	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120522	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120523	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120524	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120525	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120526	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120527	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120528	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120529	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120530	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120531	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120532	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120533	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120534	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120535	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120536	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120537	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120538	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120539	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120540	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120541	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120542	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120543	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120544	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120545	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120546	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120547	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120548	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120549	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120550	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120551	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120552	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120553	.	C	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	120554	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120555	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120556	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120557	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120558	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120559	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120560	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120561	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	120562	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120563	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120564	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120565	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120566	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120567	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120568	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120569	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120570	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120571	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	120572	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120573	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	120574	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120575	.	T	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	120576	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120577	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	120578	.	C	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4	PL	4
+Chr1	120594	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120595	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120596	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120597	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120598	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120599	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120600	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120601	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120602	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120603	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120604	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120605	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120606	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120607	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	120608	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120609	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120610	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120611	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120612	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120613	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120614	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120615	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120616	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120617	.	T	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	120618	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120619	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120620	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120621	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120622	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120623	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120624	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120625	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120626	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120627	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120628	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120629	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120630	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120631	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120632	.	C	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	120633	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120634	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	120635	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120636	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120637	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120638	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120639	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120640	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120641	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120642	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120643	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120644	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	120645	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120646	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	120647	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120648	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120649	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120650	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120651	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120652	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120653	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120654	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120655	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120656	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120657	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120658	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120659	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120660	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120661	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120662	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120663	.	T	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	120664	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	120665	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120666	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120667	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120668	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120669	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120670	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120671	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120672	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120673	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120674	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120675	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	120676	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	120677	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120678	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120679	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120680	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120681	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120682	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	120683	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	120684	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120685	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	120686	.	T	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	120687	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120688	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	120689	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120690	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	120691	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	120692	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4	PL	4
+Chr1	120693	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4	PL	0
+Chr1	1072445	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=8;FQ=-31.4	PL	4
+Chr1	1072446	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4	PL	0
+Chr1	1072447	.	C	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4	PL	0
+Chr1	1072448	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4	PL	0
+Chr1	1072449	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=8;FQ=-31.4	PL	4
+Chr1	1072450	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4	PL	0
+Chr1	1072451	.	T	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=8;FQ=-31.4	PL	4
+Chr1	1072452	.	T	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4	PL	0
+Chr1	1072453	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=8;FQ=-31.4	PL	4
+Chr1	1072454	.	A	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=8;FQ=-31.4	PL	4
+Chr1	1072455	.	G	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=8;FQ=-31.4	PL	4
+Chr1	1072456	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4	PL	0
+Chr1	1072457	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4	PL	0
+Chr1	1072458	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4	PL	0
+Chr1	1072459	.	T	.	26	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=8;FQ=-31.4	PL	4
+Chr1	1072460	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4	PL	0
+Chr1	1072461	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4	PL	0
+Chr1	1072461	.	A	.	33.5	.	INDEL;IS=1,1.000000;DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=8;FQ=-39	PL	4
+Chr1	1072462	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4	PL	0
+Chr1	1072463	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4	PL	0
+Chr1	1072464	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4	PL	0
+Chr1	1072465	.	A	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4	PL	0
+Chr1	1072466	.	G	.	31.5	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4	PL	0
+Chr1	1072467	.	A	.	32	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31	PL	0
+Chr1	1072468	.	G	.	32.4	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6	PL	0
+Chr1	1072469	.	G	.	32.4	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6	PL	0
+Chr1	1072470	.	A	.	32.4	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6	PL	0
+Chr1	1072471	.	T	.	32.4	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6	PL	0
+Chr1	1072472	.	C	.	32.4	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6	PL	0
+Chr1	1072473	.	C	.	32.4	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6	PL	0
+Chr1	1072474	.	A	.	32.4	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6	PL	0
+Chr1	1072475	.	G	.	32.4	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6	PL	0
+Chr1	1072476	.	T	.	32.4	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6	PL	0
+Chr1	1072477	.	A	.	32.4	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6	PL	0
+Chr1	1072478	.	A	.	32.4	.	DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6	PL	0
diff -r be070a68521e -r b321e0517be3 test-data/mpileup_vcf_to_gff_output.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpileup_vcf_to_gff_output.gff	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,436 @@
+#gff-version 3
+Chr1	SAMTOOLS	SNP	14086	14086	31.5	.	.	ID=Chr1:SNP:14086;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14087	14087	26	.	.	ID=Chr1:SNP:14087;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14088	14088	31.5	.	.	ID=Chr1:SNP:14088;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14089	14089	31.5	.	.	ID=Chr1:SNP:14089;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14090	14090	31.5	.	.	ID=Chr1:SNP:14090;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14091	14091	26	.	.	ID=Chr1:SNP:14091;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14092	14092	26	.	.	ID=Chr1:SNP:14092;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14093	14093	31.5	.	.	ID=Chr1:SNP:14093;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14094	14094	31.5	.	.	ID=Chr1:SNP:14094;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14095	14095	31.5	.	.	ID=Chr1:SNP:14095;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14096	14096	31.5	.	.	ID=Chr1:SNP:14096;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14097	14097	31.5	.	.	ID=Chr1:SNP:14097;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14098	14098	31.5	.	.	ID=Chr1:SNP:14098;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14099	14099	31.5	.	.	ID=Chr1:SNP:14099;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14100	14100	31.5	.	.	ID=Chr1:SNP:14100;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14101	14101	31.5	.	.	ID=Chr1:SNP:14101;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14102	14102	31.5	.	.	ID=Chr1:SNP:14102;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14103	14103	26	.	.	ID=Chr1:SNP:14103;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14104	14104	31.5	.	.	ID=Chr1:SNP:14104;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14105	14105	26	.	.	ID=Chr1:SNP:14105;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14106	14106	31.5	.	.	ID=Chr1:SNP:14106;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14107	14107	31.5	.	.	ID=Chr1:SNP:14107;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14108	14108	31.5	.	.	ID=Chr1:SNP:14108;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14109	14109	31.5	.	.	ID=Chr1:SNP:14109;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14110	14110	31.5	.	.	ID=Chr1:SNP:14110;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14111	14111	31.5	.	.	ID=Chr1:SNP:14111;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14112	14112	31.5	.	.	ID=Chr1:SNP:14112;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14113	14113	31.5	.	.	ID=Chr1:SNP:14113;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14114	14114	31.5	.	.	ID=Chr1:SNP:14114;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14115	14115	31.5	.	.	ID=Chr1:SNP:14115;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14116	14116	31.5	.	.	ID=Chr1:SNP:14116;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14117	14117	31.5	.	.	ID=Chr1:SNP:14117;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14118	14118	31.5	.	.	ID=Chr1:SNP:14118;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14119	14119	26	.	.	ID=Chr1:SNP:14119;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14120	14120	31.5	.	.	ID=Chr1:SNP:14120;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14121	14121	31.5	.	.	ID=Chr1:SNP:14121;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14122	14122	31.5	.	.	ID=Chr1:SNP:14122;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14123	14123	31.5	.	.	ID=Chr1:SNP:14123;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14124	14124	31.5	.	.	ID=Chr1:SNP:14124;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14125	14125	31.5	.	.	ID=Chr1:SNP:14125;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14126	14126	26	.	.	ID=Chr1:SNP:14126;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14127	14127	31.5	.	.	ID=Chr1:SNP:14127;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14128	14128	31.5	.	.	ID=Chr1:SNP:14128;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14129	14129	31.5	.	.	ID=Chr1:SNP:14129;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14130	14130	31.5	.	.	ID=Chr1:SNP:14130;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14131	14131	26	.	.	ID=Chr1:SNP:14131;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14132	14132	31.5	.	.	ID=Chr1:SNP:14132;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14133	14133	26	.	.	ID=Chr1:SNP:14133;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14134	14134	31.5	.	.	ID=Chr1:SNP:14134;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14135	14135	31.5	.	.	ID=Chr1:SNP:14135;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14136	14136	26	.	.	ID=Chr1:SNP:14136;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14137	14137	31.5	.	.	ID=Chr1:SNP:14137;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14138	14138	31.5	.	.	ID=Chr1:SNP:14138;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14139	14139	31.5	.	.	ID=Chr1:SNP:14139;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14140	14140	31.5	.	.	ID=Chr1:SNP:14140;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14141	14141	26	.	.	ID=Chr1:SNP:14141;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14142	14142	31.5	.	.	ID=Chr1:SNP:14142;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14143	14143	26	.	.	ID=Chr1:SNP:14143;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14144	14144	31.5	.	.	ID=Chr1:SNP:14144;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14145	14145	31.5	.	.	ID=Chr1:SNP:14145;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14146	14146	31.5	.	.	ID=Chr1:SNP:14146;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14147	14147	31.5	.	.	ID=Chr1:SNP:14147;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14148	14148	31.5	.	.	ID=Chr1:SNP:14148;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14149	14149	31.5	.	.	ID=Chr1:SNP:14149;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14150	14150	31.5	.	.	ID=Chr1:SNP:14150;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14151	14151	31.5	.	.	ID=Chr1:SNP:14151;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14152	14152	31.5	.	.	ID=Chr1:SNP:14152;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14153	14153	31.5	.	.	ID=Chr1:SNP:14153;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14154	14154	31.5	.	.	ID=Chr1:SNP:14154;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14155	14155	31.5	.	.	ID=Chr1:SNP:14155;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14156	14156	31.5	.	.	ID=Chr1:SNP:14156;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14157	14157	31.5	.	.	ID=Chr1:SNP:14157;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14158	14158	31.5	.	.	ID=Chr1:SNP:14158;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14159	14159	26	.	.	ID=Chr1:SNP:14159;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14160	14160	31.5	.	.	ID=Chr1:SNP:14160;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14161	14161	31.5	.	.	ID=Chr1:SNP:14161;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14162	14162	31.5	.	.	ID=Chr1:SNP:14162;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14163	14163	31.5	.	.	ID=Chr1:SNP:14163;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14164	14164	31.5	.	.	ID=Chr1:SNP:14164;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14165	14165	31.5	.	.	ID=Chr1:SNP:14165;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14166	14166	31.5	.	.	ID=Chr1:SNP:14166;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14167	14167	26	.	.	ID=Chr1:SNP:14167;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14168	14168	31.5	.	.	ID=Chr1:SNP:14168;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14169	14169	31.5	.	.	ID=Chr1:SNP:14169;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14170	14170	31.5	.	.	ID=Chr1:SNP:14170;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14171	14171	31.5	.	.	ID=Chr1:SNP:14171;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14172	14172	31.5	.	.	ID=Chr1:SNP:14172;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14173	14173	31.5	.	.	ID=Chr1:SNP:14173;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14174	14174	31.5	.	.	ID=Chr1:SNP:14174;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14175	14175	31.5	.	.	ID=Chr1:SNP:14175;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14176	14176	31.5	.	.	ID=Chr1:SNP:14176;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14177	14177	31.5	.	.	ID=Chr1:SNP:14177;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14178	14178	31.5	.	.	ID=Chr1:SNP:14178;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14179	14179	31.5	.	.	ID=Chr1:SNP:14179;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14180	14180	31.5	.	.	ID=Chr1:SNP:14180;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14181	14181	31.5	.	.	ID=Chr1:SNP:14181;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14182	14182	26	.	.	ID=Chr1:SNP:14182;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14183	14183	31.5	.	.	ID=Chr1:SNP:14183;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14184	14184	31.5	.	.	ID=Chr1:SNP:14184;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14185	14185	31.5	.	.	ID=Chr1:SNP:14185;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14230	14230	26	.	.	ID=Chr1:SNP:14230;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14231	14231	31.5	.	.	ID=Chr1:SNP:14231;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14232	14232	31.5	.	.	ID=Chr1:SNP:14232;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14233	14233	31.5	.	.	ID=Chr1:SNP:14233;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14234	14234	31.5	.	.	ID=Chr1:SNP:14234;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14235	14235	31.5	.	.	ID=Chr1:SNP:14235;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14236	14236	31.5	.	.	ID=Chr1:SNP:14236;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14237	14237	31.5	.	.	ID=Chr1:SNP:14237;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14238	14238	31.5	.	.	ID=Chr1:SNP:14238;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14239	14239	31.5	.	.	ID=Chr1:SNP:14239;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14240	14240	26	.	.	ID=Chr1:SNP:14240;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14241	14241	31.5	.	.	ID=Chr1:SNP:14241;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14242	14242	31.5	.	.	ID=Chr1:SNP:14242;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14243	14243	31.5	.	.	ID=Chr1:SNP:14243;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14244	14244	31.5	.	.	ID=Chr1:SNP:14244;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14245	14245	31.5	.	.	ID=Chr1:SNP:14245;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14246	14246	31.5	.	.	ID=Chr1:SNP:14246;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14247	14247	26	.	.	ID=Chr1:SNP:14247;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14248	14248	31.5	.	.	ID=Chr1:SNP:14248;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14249	14249	31.5	.	.	ID=Chr1:SNP:14249;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14250	14250	31.5	.	.	ID=Chr1:SNP:14250;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14251	14251	31.5	.	.	ID=Chr1:SNP:14251;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14252	14252	31.5	.	.	ID=Chr1:SNP:14252;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14253	14253	31.5	.	.	ID=Chr1:SNP:14253;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14254	14254	31.5	.	.	ID=Chr1:SNP:14254;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14255	14255	31.5	.	.	ID=Chr1:SNP:14255;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14256	14256	26	.	.	ID=Chr1:SNP:14256;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14257	14257	31.5	.	.	ID=Chr1:SNP:14257;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14258	14258	31.5	.	.	ID=Chr1:SNP:14258;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14259	14259	31.5	.	.	ID=Chr1:SNP:14259;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14260	14260	31.5	.	.	ID=Chr1:SNP:14260;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14261	14261	31.5	.	.	ID=Chr1:SNP:14261;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14262	14262	26	.	.	ID=Chr1:SNP:14262;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14263	14263	26	.	.	ID=Chr1:SNP:14263;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14264	14264	31.5	.	.	ID=Chr1:SNP:14264;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14265	14265	31.5	.	.	ID=Chr1:SNP:14265;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14266	14266	31.5	.	.	ID=Chr1:SNP:14266;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14267	14267	31.5	.	.	ID=Chr1:SNP:14267;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14268	14268	31.5	.	.	ID=Chr1:SNP:14268;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14269	14269	31.5	.	.	ID=Chr1:SNP:14269;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14270	14270	31.5	.	.	ID=Chr1:SNP:14270;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14271	14271	31.5	.	.	ID=Chr1:SNP:14271;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14272	14272	31.5	.	.	ID=Chr1:SNP:14272;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14273	14273	31.5	.	.	ID=Chr1:SNP:14273;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14274	14274	31.5	.	.	ID=Chr1:SNP:14274;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14275	14275	31.5	.	.	ID=Chr1:SNP:14275;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14276	14276	31.5	.	.	ID=Chr1:SNP:14276;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14277	14277	31.5	.	.	ID=Chr1:SNP:14277;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14278	14278	31.5	.	.	ID=Chr1:SNP:14278;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14279	14279	31.5	.	.	ID=Chr1:SNP:14279;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14280	14280	31.5	.	.	ID=Chr1:SNP:14280;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14281	14281	31.5	.	.	ID=Chr1:SNP:14281;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14282	14282	31.5	.	.	ID=Chr1:SNP:14282;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14283	14283	31.5	.	.	ID=Chr1:SNP:14283;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14284	14284	31.5	.	.	ID=Chr1:SNP:14284;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14285	14285	31.5	.	.	ID=Chr1:SNP:14285;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14286	14286	31.5	.	.	ID=Chr1:SNP:14286;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14287	14287	31.5	.	.	ID=Chr1:SNP:14287;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14288	14288	31.5	.	.	ID=Chr1:SNP:14288;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14289	14289	31.5	.	.	ID=Chr1:SNP:14289;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14290	14290	31.5	.	.	ID=Chr1:SNP:14290;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14291	14291	31.5	.	.	ID=Chr1:SNP:14291;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14292	14292	26	.	.	ID=Chr1:SNP:14292;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14293	14293	31.5	.	.	ID=Chr1:SNP:14293;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14294	14294	31.5	.	.	ID=Chr1:SNP:14294;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14295	14295	26	.	.	ID=Chr1:SNP:14295;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14296	14296	31.5	.	.	ID=Chr1:SNP:14296;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14297	14297	31.5	.	.	ID=Chr1:SNP:14297;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14298	14298	31.5	.	.	ID=Chr1:SNP:14298;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14299	14299	31.5	.	.	ID=Chr1:SNP:14299;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14300	14300	31.5	.	.	ID=Chr1:SNP:14300;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14301	14301	31.5	.	.	ID=Chr1:SNP:14301;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14302	14302	31.5	.	.	ID=Chr1:SNP:14302;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14303	14303	31.5	.	.	ID=Chr1:SNP:14303;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14304	14304	31.5	.	.	ID=Chr1:SNP:14304;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14305	14305	31.5	.	.	ID=Chr1:SNP:14305;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14306	14306	26	.	.	ID=Chr1:SNP:14306;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14307	14307	26	.	.	ID=Chr1:SNP:14307;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14308	14308	31.5	.	.	ID=Chr1:SNP:14308;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14309	14309	31.5	.	.	ID=Chr1:SNP:14309;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14310	14310	31.5	.	.	ID=Chr1:SNP:14310;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14311	14311	31.5	.	.	ID=Chr1:SNP:14311;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14312	14312	26	.	.	ID=Chr1:SNP:14312;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14313	14313	26	.	.	ID=Chr1:SNP:14313;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14314	14314	31.5	.	.	ID=Chr1:SNP:14314;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14315	14315	31.5	.	.	ID=Chr1:SNP:14315;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14316	14316	31.5	.	.	ID=Chr1:SNP:14316;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14317	14317	31.5	.	.	ID=Chr1:SNP:14317;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14318	14318	31.5	.	.	ID=Chr1:SNP:14318;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14319	14319	31.5	.	.	ID=Chr1:SNP:14319;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14320	14320	31.5	.	.	ID=Chr1:SNP:14320;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	INDEL	14320	14322	33.5	.	.	ID=Chr1:INDEL:14320;Variant_seq=.;Reference_seq=TC;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14321	14321	31.5	.	.	ID=Chr1:SNP:14321;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14322	14322	26	.	.	ID=Chr1:SNP:14322;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14323	14323	31.5	.	.	ID=Chr1:SNP:14323;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14324	14324	26	.	.	ID=Chr1:SNP:14324;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14325	14325	31.5	.	.	ID=Chr1:SNP:14325;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14326	14326	31.5	.	.	ID=Chr1:SNP:14326;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14327	14327	26	.	.	ID=Chr1:SNP:14327;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	14328	14328	31.5	.	.	ID=Chr1:SNP:14328;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120479	120479	31.5	.	.	ID=Chr1:SNP:120479;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120480	120480	31.5	.	.	ID=Chr1:SNP:120480;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120481	120481	31.5	.	.	ID=Chr1:SNP:120481;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120482	120482	31.5	.	.	ID=Chr1:SNP:120482;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120483	120483	31.5	.	.	ID=Chr1:SNP:120483;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120484	120484	31.5	.	.	ID=Chr1:SNP:120484;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120485	120485	31.5	.	.	ID=Chr1:SNP:120485;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120486	120486	31.5	.	.	ID=Chr1:SNP:120486;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120487	120487	31.5	.	.	ID=Chr1:SNP:120487;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120488	120488	31.5	.	.	ID=Chr1:SNP:120488;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120489	120489	31.5	.	.	ID=Chr1:SNP:120489;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120490	120490	31.5	.	.	ID=Chr1:SNP:120490;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120491	120491	31.5	.	.	ID=Chr1:SNP:120491;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120492	120492	31.5	.	.	ID=Chr1:SNP:120492;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120493	120493	31.5	.	.	ID=Chr1:SNP:120493;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120494	120494	31.5	.	.	ID=Chr1:SNP:120494;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120495	120495	31.5	.	.	ID=Chr1:SNP:120495;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120496	120496	31.5	.	.	ID=Chr1:SNP:120496;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120497	120497	31.5	.	.	ID=Chr1:SNP:120497;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120498	120498	26	.	.	ID=Chr1:SNP:120498;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120499	120499	31.5	.	.	ID=Chr1:SNP:120499;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120500	120500	31.5	.	.	ID=Chr1:SNP:120500;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120501	120501	31.5	.	.	ID=Chr1:SNP:120501;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120502	120502	31.5	.	.	ID=Chr1:SNP:120502;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120503	120503	31.5	.	.	ID=Chr1:SNP:120503;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120504	120504	31.5	.	.	ID=Chr1:SNP:120504;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120505	120505	31.5	.	.	ID=Chr1:SNP:120505;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120506	120506	31.5	.	.	ID=Chr1:SNP:120506;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120507	120507	31.5	.	.	ID=Chr1:SNP:120507;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120508	120508	26	.	.	ID=Chr1:SNP:120508;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120509	120509	31.5	.	.	ID=Chr1:SNP:120509;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120510	120510	31.5	.	.	ID=Chr1:SNP:120510;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120511	120511	31.5	.	.	ID=Chr1:SNP:120511;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120512	120512	31.5	.	.	ID=Chr1:SNP:120512;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120513	120513	31.5	.	.	ID=Chr1:SNP:120513;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120514	120514	31.5	.	.	ID=Chr1:SNP:120514;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120515	120515	26	.	.	ID=Chr1:SNP:120515;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120516	120516	31.5	.	.	ID=Chr1:SNP:120516;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120517	120517	31.5	.	.	ID=Chr1:SNP:120517;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120518	120518	26	.	.	ID=Chr1:SNP:120518;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120519	120519	31.5	.	.	ID=Chr1:SNP:120519;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120520	120520	31.5	.	.	ID=Chr1:SNP:120520;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120521	120521	31.5	.	.	ID=Chr1:SNP:120521;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120522	120522	31.5	.	.	ID=Chr1:SNP:120522;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120523	120523	31.5	.	.	ID=Chr1:SNP:120523;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120524	120524	31.5	.	.	ID=Chr1:SNP:120524;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120525	120525	31.5	.	.	ID=Chr1:SNP:120525;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120526	120526	31.5	.	.	ID=Chr1:SNP:120526;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120527	120527	31.5	.	.	ID=Chr1:SNP:120527;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120528	120528	31.5	.	.	ID=Chr1:SNP:120528;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120529	120529	31.5	.	.	ID=Chr1:SNP:120529;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120530	120530	31.5	.	.	ID=Chr1:SNP:120530;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120531	120531	31.5	.	.	ID=Chr1:SNP:120531;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120532	120532	31.5	.	.	ID=Chr1:SNP:120532;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120533	120533	31.5	.	.	ID=Chr1:SNP:120533;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120534	120534	31.5	.	.	ID=Chr1:SNP:120534;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120535	120535	31.5	.	.	ID=Chr1:SNP:120535;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120536	120536	31.5	.	.	ID=Chr1:SNP:120536;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120537	120537	31.5	.	.	ID=Chr1:SNP:120537;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120538	120538	31.5	.	.	ID=Chr1:SNP:120538;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120539	120539	31.5	.	.	ID=Chr1:SNP:120539;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120540	120540	31.5	.	.	ID=Chr1:SNP:120540;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120541	120541	31.5	.	.	ID=Chr1:SNP:120541;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120542	120542	31.5	.	.	ID=Chr1:SNP:120542;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120543	120543	31.5	.	.	ID=Chr1:SNP:120543;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120544	120544	31.5	.	.	ID=Chr1:SNP:120544;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120545	120545	31.5	.	.	ID=Chr1:SNP:120545;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120546	120546	31.5	.	.	ID=Chr1:SNP:120546;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120547	120547	31.5	.	.	ID=Chr1:SNP:120547;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120548	120548	31.5	.	.	ID=Chr1:SNP:120548;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120549	120549	31.5	.	.	ID=Chr1:SNP:120549;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120550	120550	31.5	.	.	ID=Chr1:SNP:120550;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120551	120551	31.5	.	.	ID=Chr1:SNP:120551;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120552	120552	31.5	.	.	ID=Chr1:SNP:120552;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120553	120553	26	.	.	ID=Chr1:SNP:120553;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120554	120554	31.5	.	.	ID=Chr1:SNP:120554;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120555	120555	31.5	.	.	ID=Chr1:SNP:120555;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120556	120556	31.5	.	.	ID=Chr1:SNP:120556;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120557	120557	31.5	.	.	ID=Chr1:SNP:120557;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120558	120558	31.5	.	.	ID=Chr1:SNP:120558;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120559	120559	31.5	.	.	ID=Chr1:SNP:120559;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120560	120560	31.5	.	.	ID=Chr1:SNP:120560;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120561	120561	26	.	.	ID=Chr1:SNP:120561;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120562	120562	31.5	.	.	ID=Chr1:SNP:120562;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120563	120563	31.5	.	.	ID=Chr1:SNP:120563;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120564	120564	31.5	.	.	ID=Chr1:SNP:120564;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120565	120565	31.5	.	.	ID=Chr1:SNP:120565;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120566	120566	31.5	.	.	ID=Chr1:SNP:120566;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120567	120567	31.5	.	.	ID=Chr1:SNP:120567;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120568	120568	31.5	.	.	ID=Chr1:SNP:120568;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120569	120569	31.5	.	.	ID=Chr1:SNP:120569;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120570	120570	31.5	.	.	ID=Chr1:SNP:120570;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120571	120571	26	.	.	ID=Chr1:SNP:120571;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120572	120572	31.5	.	.	ID=Chr1:SNP:120572;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120573	120573	26	.	.	ID=Chr1:SNP:120573;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120574	120574	31.5	.	.	ID=Chr1:SNP:120574;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120575	120575	26	.	.	ID=Chr1:SNP:120575;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120576	120576	31.5	.	.	ID=Chr1:SNP:120576;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120577	120577	26	.	.	ID=Chr1:SNP:120577;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120578	120578	26	.	.	ID=Chr1:SNP:120578;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120594	120594	31.5	.	.	ID=Chr1:SNP:120594;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120595	120595	31.5	.	.	ID=Chr1:SNP:120595;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120596	120596	31.5	.	.	ID=Chr1:SNP:120596;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120597	120597	31.5	.	.	ID=Chr1:SNP:120597;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120598	120598	31.5	.	.	ID=Chr1:SNP:120598;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120599	120599	31.5	.	.	ID=Chr1:SNP:120599;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120600	120600	31.5	.	.	ID=Chr1:SNP:120600;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120601	120601	31.5	.	.	ID=Chr1:SNP:120601;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120602	120602	31.5	.	.	ID=Chr1:SNP:120602;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120603	120603	31.5	.	.	ID=Chr1:SNP:120603;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120604	120604	31.5	.	.	ID=Chr1:SNP:120604;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120605	120605	31.5	.	.	ID=Chr1:SNP:120605;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120606	120606	31.5	.	.	ID=Chr1:SNP:120606;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120607	120607	26	.	.	ID=Chr1:SNP:120607;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120608	120608	31.5	.	.	ID=Chr1:SNP:120608;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120609	120609	31.5	.	.	ID=Chr1:SNP:120609;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120610	120610	31.5	.	.	ID=Chr1:SNP:120610;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120611	120611	31.5	.	.	ID=Chr1:SNP:120611;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120612	120612	31.5	.	.	ID=Chr1:SNP:120612;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120613	120613	31.5	.	.	ID=Chr1:SNP:120613;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120614	120614	31.5	.	.	ID=Chr1:SNP:120614;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120615	120615	31.5	.	.	ID=Chr1:SNP:120615;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120616	120616	31.5	.	.	ID=Chr1:SNP:120616;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120617	120617	26	.	.	ID=Chr1:SNP:120617;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120618	120618	31.5	.	.	ID=Chr1:SNP:120618;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120619	120619	31.5	.	.	ID=Chr1:SNP:120619;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120620	120620	31.5	.	.	ID=Chr1:SNP:120620;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120621	120621	31.5	.	.	ID=Chr1:SNP:120621;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120622	120622	31.5	.	.	ID=Chr1:SNP:120622;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120623	120623	31.5	.	.	ID=Chr1:SNP:120623;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120624	120624	31.5	.	.	ID=Chr1:SNP:120624;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120625	120625	31.5	.	.	ID=Chr1:SNP:120625;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120626	120626	31.5	.	.	ID=Chr1:SNP:120626;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120627	120627	31.5	.	.	ID=Chr1:SNP:120627;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120628	120628	31.5	.	.	ID=Chr1:SNP:120628;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120629	120629	31.5	.	.	ID=Chr1:SNP:120629;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120630	120630	31.5	.	.	ID=Chr1:SNP:120630;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120631	120631	31.5	.	.	ID=Chr1:SNP:120631;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120632	120632	26	.	.	ID=Chr1:SNP:120632;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120633	120633	31.5	.	.	ID=Chr1:SNP:120633;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120634	120634	26	.	.	ID=Chr1:SNP:120634;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120635	120635	31.5	.	.	ID=Chr1:SNP:120635;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120636	120636	31.5	.	.	ID=Chr1:SNP:120636;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120637	120637	31.5	.	.	ID=Chr1:SNP:120637;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120638	120638	31.5	.	.	ID=Chr1:SNP:120638;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120639	120639	31.5	.	.	ID=Chr1:SNP:120639;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120640	120640	31.5	.	.	ID=Chr1:SNP:120640;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120641	120641	31.5	.	.	ID=Chr1:SNP:120641;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120642	120642	31.5	.	.	ID=Chr1:SNP:120642;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120643	120643	31.5	.	.	ID=Chr1:SNP:120643;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120644	120644	26	.	.	ID=Chr1:SNP:120644;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120645	120645	31.5	.	.	ID=Chr1:SNP:120645;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120646	120646	26	.	.	ID=Chr1:SNP:120646;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120647	120647	31.5	.	.	ID=Chr1:SNP:120647;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120648	120648	31.5	.	.	ID=Chr1:SNP:120648;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120649	120649	31.5	.	.	ID=Chr1:SNP:120649;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120650	120650	31.5	.	.	ID=Chr1:SNP:120650;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120651	120651	31.5	.	.	ID=Chr1:SNP:120651;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120652	120652	31.5	.	.	ID=Chr1:SNP:120652;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120653	120653	31.5	.	.	ID=Chr1:SNP:120653;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120654	120654	31.5	.	.	ID=Chr1:SNP:120654;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120655	120655	31.5	.	.	ID=Chr1:SNP:120655;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120656	120656	31.5	.	.	ID=Chr1:SNP:120656;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120657	120657	31.5	.	.	ID=Chr1:SNP:120657;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120658	120658	31.5	.	.	ID=Chr1:SNP:120658;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120659	120659	31.5	.	.	ID=Chr1:SNP:120659;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120660	120660	31.5	.	.	ID=Chr1:SNP:120660;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120661	120661	31.5	.	.	ID=Chr1:SNP:120661;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120662	120662	31.5	.	.	ID=Chr1:SNP:120662;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120663	120663	26	.	.	ID=Chr1:SNP:120663;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120664	120664	26	.	.	ID=Chr1:SNP:120664;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120665	120665	31.5	.	.	ID=Chr1:SNP:120665;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120666	120666	31.5	.	.	ID=Chr1:SNP:120666;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120667	120667	31.5	.	.	ID=Chr1:SNP:120667;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120668	120668	31.5	.	.	ID=Chr1:SNP:120668;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120669	120669	31.5	.	.	ID=Chr1:SNP:120669;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120670	120670	31.5	.	.	ID=Chr1:SNP:120670;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120671	120671	31.5	.	.	ID=Chr1:SNP:120671;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120672	120672	31.5	.	.	ID=Chr1:SNP:120672;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120673	120673	31.5	.	.	ID=Chr1:SNP:120673;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120674	120674	31.5	.	.	ID=Chr1:SNP:120674;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120675	120675	26	.	.	ID=Chr1:SNP:120675;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120676	120676	26	.	.	ID=Chr1:SNP:120676;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120677	120677	31.5	.	.	ID=Chr1:SNP:120677;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120678	120678	31.5	.	.	ID=Chr1:SNP:120678;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120679	120679	31.5	.	.	ID=Chr1:SNP:120679;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120680	120680	31.5	.	.	ID=Chr1:SNP:120680;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120681	120681	31.5	.	.	ID=Chr1:SNP:120681;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120682	120682	26	.	.	ID=Chr1:SNP:120682;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120683	120683	26	.	.	ID=Chr1:SNP:120683;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120684	120684	31.5	.	.	ID=Chr1:SNP:120684;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120685	120685	26	.	.	ID=Chr1:SNP:120685;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120686	120686	26	.	.	ID=Chr1:SNP:120686;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120687	120687	31.5	.	.	ID=Chr1:SNP:120687;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120688	120688	26	.	.	ID=Chr1:SNP:120688;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120689	120689	31.5	.	.	ID=Chr1:SNP:120689;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120690	120690	26	.	.	ID=Chr1:SNP:120690;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120691	120691	31.5	.	.	ID=Chr1:SNP:120691;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120692	120692	26	.	.	ID=Chr1:SNP:120692;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	120693	120693	31.5	.	.	ID=Chr1:SNP:120693;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072445	1072445	26	.	.	ID=Chr1:SNP:1072445;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072446	1072446	31.5	.	.	ID=Chr1:SNP:1072446;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072447	1072447	31.5	.	.	ID=Chr1:SNP:1072447;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072448	1072448	31.5	.	.	ID=Chr1:SNP:1072448;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072449	1072449	26	.	.	ID=Chr1:SNP:1072449;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072450	1072450	31.5	.	.	ID=Chr1:SNP:1072450;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072451	1072451	26	.	.	ID=Chr1:SNP:1072451;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072452	1072452	31.5	.	.	ID=Chr1:SNP:1072452;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072453	1072453	26	.	.	ID=Chr1:SNP:1072453;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072454	1072454	26	.	.	ID=Chr1:SNP:1072454;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072455	1072455	26	.	.	ID=Chr1:SNP:1072455;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072456	1072456	31.5	.	.	ID=Chr1:SNP:1072456;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072457	1072457	31.5	.	.	ID=Chr1:SNP:1072457;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072458	1072458	31.5	.	.	ID=Chr1:SNP:1072458;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072459	1072459	26	.	.	ID=Chr1:SNP:1072459;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072460	1072460	31.5	.	.	ID=Chr1:SNP:1072460;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072461	1072461	31.5	.	.	ID=Chr1:SNP:1072461;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	INDEL	1072461	1072462	33.5	.	.	ID=Chr1:INDEL:1072461;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072462	1072462	31.5	.	.	ID=Chr1:SNP:1072462;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072463	1072463	31.5	.	.	ID=Chr1:SNP:1072463;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072464	1072464	31.5	.	.	ID=Chr1:SNP:1072464;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072465	1072465	31.5	.	.	ID=Chr1:SNP:1072465;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072466	1072466	31.5	.	.	ID=Chr1:SNP:1072466;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072467	1072467	32	.	.	ID=Chr1:SNP:1072467;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072468	1072468	32.4	.	.	ID=Chr1:SNP:1072468;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072469	1072469	32.4	.	.	ID=Chr1:SNP:1072469;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072470	1072470	32.4	.	.	ID=Chr1:SNP:1072470;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072471	1072471	32.4	.	.	ID=Chr1:SNP:1072471;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072472	1072472	32.4	.	.	ID=Chr1:SNP:1072472;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072473	1072473	32.4	.	.	ID=Chr1:SNP:1072473;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072474	1072474	32.4	.	.	ID=Chr1:SNP:1072474;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072475	1072475	32.4	.	.	ID=Chr1:SNP:1072475;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072476	1072476	32.4	.	.	ID=Chr1:SNP:1072476;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072477	1072477	32.4	.	.	ID=Chr1:SNP:1072477;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
+Chr1	SAMTOOLS	SNP	1072478	1072478	32.4	.	.	ID=Chr1:SNP:1072478;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA 
diff -r be070a68521e -r b321e0517be3 test-data/targets
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/targets	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,5 @@
+k69_93535:SAMTOOLS:SNP:1147
+k69_93535:SAMTOOLS:SNP:1336
+k69_98089:SAMTOOLS:SNP:30
+k69_98089:SAMTOOLS:SNP:550
+k69_98089:SAMTOOLS:SNP:625
diff -r be070a68521e -r b321e0517be3 test-data/targets.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/targets.fasta	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,44 @@
+>k69_93535
+TCATCAAATTTATCAAATTTTCCGCAGTTTCTCGCCCTCTCCACAGCGCTTTGAAGCGCT
+TTTAATGGCAGCAGATGCCGCCTCAGATCTCCCAAACCGACCCATTCCTAACACTCTCAG
+AAGATCCGATTCCAATTCCGTTCTACTGAACAAATACGAGCTGGGCAAGCTCCTCGGCCA
+TGGAAATTTCGCCAAGGTTTACCTCGCCCGCAACCTCGCCTCCAACGAAGAAGTCGCTAT
+CAAAGTCTTCGACAAAGAGAAAATCCTCAAATCCGGCCTCGTCAACCACACCAAACGCGA
+GATCTCAATCCTCCGCCGTCTTCGTCATCCGAACGTCGTCGAGCTCTTCGAGGTCATGGC
+CACTAAATCGAAGATCTATTTCGTCATAGAGTACGTCCGCGGTGGTGAATTATTCGGCAA
+GGTAGCCAAAGGACGTCTCAACGAAAACACCGCAAGAAAGTACTTCCAGCAATTGATTTC
+CGCCGTTGATTTCTGCCACGCCAGAGGCGTTTACCACAGAGATCTGAAGCCGGAAAATTT
+ATTATTAGACGATAATGGTGATTTGAAGGTGTCGGATTTCGGATTGAGCGCTGTATCGGA
+CCAGATGAGGCAGGATGGGTTGTTTCACACGTTTTGTGGTACTCCAGCCTACGTTGCTCC
+AGAGGTTCTCGGAAGGAAAGGGTATGATGGGGCTAAGTTTGATATTTGGTCATGTGGTGT
+TATTTTGTTTTTGTTGATGGCAGGGTATTTGCCCTTTCATGATCAAAATGTGATGGCTAT
+GTATAAGAAGATTTATAAAGGGGAGTTCAGGTGTCCGAGATGGTTTTCAAAGGATTTGAC
+ATTGTTGCTGATGAGGCTTCTCGATACAAATCCCAAAACCCGGATCACTATTCCAGAAAT
+AATGGAGAATAGATGGTTCAAGAATGGATTCGAGCCTGTGAAATATTACATTGAGAATGA
+TAGGTTTCATAAGTGGTGTAGCTTAGACGAAGAGAATGCTAATGACAACGAGGAGGTAGA
+ATCTGGAGATGAATCAGACTCTTCAGTTGCTTCCTGCCCTCCTACACTTAATGAAGGAAA
+GAAAAAAAGGACAGGGAAGCTTCATAGGCCTTTGAGTCTGAACGCATTTGACATAATTTC
+CTTTTCCAGAGGATTTGATCTTTCAGGTTTGTTTGAAGAAACGGGAGATGAAACAAGATT
+TGTGTCGGGTGAAACGATACCAAACATCATATCGAAATTGGAGGAGATTGCAAAAGTGGG
+TAGTTTCACGTTTAGGAAGAAGGATTGTAGGGTTAGTTTAGAAGGAACGCGAGAAGGAGT
+GAAGGGCCCTCTTACGATTGGAGCTGAGATATTTGAGCTTACGCCTAGTTTGGTTGTTGT
+TGAGCTTAAGAAGAAAGCAGGAGACAAAGCAGAGTACGAGGAGTTTTGTAACAAGGAGTT
+GAAACCTGGGTTGCTACATCTCATGTTTCCTAATGGCGGTGTTCCTTCCAACACAACTTC
+TGATACAGAGTAGGCAGTGTAGGGAATTCTCAAATGTATCTGTATTATATGGCAGCGTTT
+CATGATTCTTTTTGTATTAGATTTGTCGCAAGAAATTTATGTACCTTAAGATGAAAATTC
+AAGTTTCA
+>k69_98089
+ACAAATCCAAACATGTTATCTTCTTCTTCTTTTCCTTCTTCAAACATCCTCCTCCTCACC
+AAGTCAAAATCGCTCAACGTCAGATCATCAACACGAACTTGCGCCATGGCCACCACTGCT
+TCCCCATCTCCGTACGACGTGCTAGGCCTTTCGAAAGCCGCAAACTACAGCGACATAAAA
+GCAGCGTATCGGAAACTGGTGCTCTCCTGCCATCCCGATGTCTGCAAACAGCCGGATGCG
+TCACCGGACGAGTTTATGAAAATACACGATGCGTATTCCACGCTTTCTGATCCGGACAAG
+CGTGCCGATTACGATCGGGGAAATTCATTTGGGCGTTTGAGTTATGTGAGATCTAGATCT
+GCGAATTATGGTGCTCGTCGTCGAACTTGGGAGACCGATCAGTGTTGGTAAATCTAATTT
+GGGGGTTTGGAGATCTATTGATTTTGTTAGGAATGGAGAAGGTCGAGGTCAGCGGTCAGC
+TACGTGGGGCTAAATATTTTGAATTGATACTGAAATTCGGGAAGACTGAAAGAACGGGAT
+GATAACGGTGGTAGATCCAATTAGATTGTGGAAACTTTCATGTATGCTATCTACCTAAAA
+ATAATTGTGAATTTTGTGCCTCATAAGTTTGTTTGTTTAGGCATTTTTTGACTTCTGAGA
+CGTTGTATGTATATTCGGCCGTTACTACTTTATTGGCTTTAATGGTGTATACTTTGTTGT
+TTGCTTGTTATCCTGTACTAAATTTCT
+
diff -r be070a68521e -r b321e0517be3 test-data/targets.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/targets.gff	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,31 @@
+k69_93535	SAMTOOLS	INDEL	3	7	4.44	.	.	ID=k69_93535:SAMTOOLS:INDEL:3;Variant_seq=ATTTCACATCCCATCATCA,ATCACATCCCATCATCA;Reference_seq=ATCA;INDEL;DP=5;VDB=0.0149;AF1=1;AC1=24;DP4=0,0,3,0;MQ=23;FQ=-33.2
+k69_93535	SAMTOOLS	INDEL	5	6	4.91	.	.	ID=k69_93535:SAMTOOLS:INDEL:5;Variant_seq=CTCATATCCCATCATC,CCGGCC;Reference_seq=C;INDEL;DP=6;VDB=0.0137;AF1=1;AC1=24;DP4=0,0,3,1;MQ=17;FQ=-32.4
+k69_93535	SAMTOOLS	SNP	1141	1142	999	.	.	ID=k69_93535:SAMTOOLS:SNP:1141;Variant_seq=T;Reference_seq=C;DP=2644;VDB=0.0374;AF1=0.1882;AC1=5;DP4=748,786,225,294;MQ=42;FQ=999;PV4=0.037,0,0.036,0.39
+k69_93535	SAMTOOLS	SNP	1147	1148	999	.	.	ID=k69_93535:SAMTOOLS:SNP:1147;Variant_seq=G;Reference_seq=C;DP=2645;VDB=0.0371;AF1=0.3527;G3=0.2771,0.7229,6.934e-153;HWE=0.0248;AC1=8;DP4=733,804,447,519;MQ=42;FQ=999;PV4=0.51,0,0.027,1
+k69_93535	SAMTOOLS	SNP	1336	1337	999	.	.	ID=k69_93535:SAMTOOLS:SNP:1336;Variant_seq=A;Reference_seq=G;DP=2211;VDB=0.0395;AF1=0.4583;G3=0.08329,0.9167,1.041e-76;HWE=0.000925;AC1=11;DP4=487,645,470,542;MQ=35;FQ=999;PV4=0.12,0,0.00016,0.36
+k69_93535	SAMTOOLS	SNP	3	4	27.6	.	.	ID=k69_93535:SAMTOOLS:SNP:3;Variant_seq=T;Reference_seq=A;DP=5;VDB=0.0198;AF1=1;AC1=24;DP4=1,0,3,1;MQ=19;FQ=-24.6;PV4=1,1,1,1
+k69_93535	SAMTOOLS	SNP	661	662	999	.	.	ID=k69_93535:SAMTOOLS:SNP:661;Variant_seq=G;Reference_seq=A;DP=1941;VDB=0.0388;AF1=0.4584;G3=0.08304,0.917,5.651e-77;HWE=0.000923;AC1=11;DP4=553,528,368,347;MQ=42;FQ=999;PV4=0.92,0,1,1
+k69_93535	SAMTOOLS	SNP	751	752	999	.	.	ID=k69_93535:SAMTOOLS:SNP:751;Variant_seq=A;Reference_seq=G;DP=1870;VDB=0.0363;AF1=0.5;G3=3.472e-15,1,5e-52;HWE=4.53e-05;AC1=12;DP4=512,544,345,364;MQ=42;FQ=999;PV4=0.96,6.1e-38,0.014,1
+k69_93535	SAMTOOLS	SNP	887	888	999	.	.	ID=k69_93535:SAMTOOLS:SNP:887;Variant_seq=G;Reference_seq=A;DP=2583;VDB=0.0394;AF1=0.4583;G3=0.08333,0.9167,8.95e-52;HWE=0.000926;AC1=11;DP4=790,493,590,361;MQ=42;FQ=999;PV4=0.83,0.069,0.41,1
+k69_98089	SAMTOOLS	INDEL	2	6	999	.	.	ID=k69_98089:SAMTOOLS:INDEL:2;Variant_seq=CAACAAA,CAAACAAA,CAAAAACAAA;Reference_seq=CAAA;INDEL;DP=430;VDB=0.0000;AF1=1;AC1=24;DP4=0,0,182,1;MQ=39;FQ=-71.8
+k69_98089	SAMTOOLS	INDEL	3	6	999	.	.	ID=k69_98089:SAMTOOLS:INDEL:3;Variant_seq=AAAAAACAAA,AAAA;Reference_seq=AAA;INDEL;DP=451;VDB=0.0000;AF1=1;AC1=24;DP4=0,0,214,1;MQ=39;FQ=-48
+k69_98089	SAMTOOLS	INDEL	4	6	999	.	.	ID=k69_98089:SAMTOOLS:INDEL:4;Variant_seq=AAACACTAAAAACAAA,AAA;Reference_seq=AA;INDEL;DP=468;VDB=0.0000;AF1=1;AC1=24;DP4=0,0,219,1;MQ=39;FQ=-49.3
+k69_98089	SAMTOOLS	INDEL	5	6	999	.	.	ID=k69_98089:SAMTOOLS:INDEL:5;Variant_seq=AACTAAAAACAAA;Reference_seq=A;INDEL;DP=534;VDB=0.0000;AF1=1;AC1=24;DP4=0,0,220,1;MQ=39;FQ=-77.6
+k69_98089	SAMTOOLS	INDEL	722	723	131	.	.	ID=k69_98089:SAMTOOLS:INDEL:722;Variant_seq=TAAAAAA;Reference_seq=T;INDEL;DP=220;VDB=0.0006;AF1=0.3195;G3=0.299,0.701,1.118e-32;HWE=0.0406;AC1=8;DP4=4,52,0,27;MQ=38;FQ=133;PV4=0.3,1,5.4e-16,0.00096
+k69_98089	SAMTOOLS	INDEL	726	727	69.7	.	.	ID=k69_98089:SAMTOOLS:INDEL:726;Variant_seq=TAAAAA;Reference_seq=T;INDEL;DP=152;VDB=0.0007;AF1=0.2294;AC1=5;DP4=4,30,1,6;MQ=40;FQ=70.8;PV4=1,0.025,0.0063,0.079
+k69_98089	SAMTOOLS	INDEL	729	731	71.6	.	.	ID=k69_98089:SAMTOOLS:INDEL:729;Variant_seq=TAAAAAAA;Reference_seq=TA;INDEL;DP=104;VDB=0.0010;AF1=0.3359;AC1=8;DP4=3,15,0,4;MQ=40;FQ=73.4;PV4=1,1,1,1
+k69_98089	SAMTOOLS	INDEL	741	748	48.2	.	.	ID=k69_98089:SAMTOOLS:INDEL:741;Variant_seq=AATTTCTATTTGTTTATTATTTCT,AATTTCTATTTGTTTATTTCT,AATTTCTATTTCT;Reference_seq=AATTTCT;INDEL;DP=18;VDB=0.0050;AF1=1;AC1=24;DP4=0,0,0,9;MQ=27;FQ=-35
+k69_98089	SAMTOOLS	INDEL	742	748	5.8	.	.	ID=k69_98089:SAMTOOLS:INDEL:742;Variant_seq=ATTTTTCT,ATTTCTATTTTCT,ATTTCTATTTTTCT;Reference_seq=ATTTCT;INDEL;DP=17;VDB=0.0022;AF1=1;AC1=24;DP4=0,0,0,3;MQ=36;FQ=-31.8
+k69_98089	SAMTOOLS	INDEL	743	748	86.5	.	.	ID=k69_98089:SAMTOOLS:INDEL:743;Variant_seq=TTTCTATTTGTTCT,TTTCTATTTGTTTATTATTCT,TTTCTATTTGTTTATTCT;Reference_seq=TTTCT;INDEL;DP=16;VDB=0.0021;AF1=1;AC1=24;DP4=0,0,0,8;MQ=29;FQ=-34.7
+k69_98089	SAMTOOLS	SNP	2	3	999	.	.	ID=k69_98089:SAMTOOLS:SNP:2;Variant_seq=A;Reference_seq=C;DP=430;VDB=0.0000;AF1=0.5;G3=1.09e-24,1,5.6e-21;HWE=4.53e-05;AC1=12;DP4=207,1,212,1;MQ=40;FQ=999;PV4=1,1,0.00045,1
+k69_98089	SAMTOOLS	SNP	30	31	999	.	.	ID=k69_98089:SAMTOOLS:SNP:30;Variant_seq=G;Reference_seq=T;DP=1858;VDB=0.0011;AF1=0.5417;G3=2.023e-19,0.9167,0.08333;HWE=0.000926;AC1=13;DP4=624,74,985,116;MQ=41;FQ=999;PV4=1,0,0.00089,1
+k69_98089	SAMTOOLS	SNP	3	4	999	.	.	ID=k69_98089:SAMTOOLS:SNP:3;Variant_seq=C;Reference_seq=A;DP=451;VDB=0.0000;AF1=0.5;G3=3.935e-24,1,2.231e-22;HWE=4.53e-05;AC1=12;DP4=226,8,205,1;MQ=40;FQ=999;PV4=0.041,1,0.00055,1
+k69_98089	SAMTOOLS	SNP	453	454	31.2	.	.	ID=k69_98089:SAMTOOLS:SNP:453;Variant_seq=T;Reference_seq=A;DP=3692;VDB=0.0394;AF1=0.04171;AC1=1;DP4=649,868,130,171;MQ=39;FQ=31.4;PV4=0.9,0,2.3e-293,0.00051
+k69_98089	SAMTOOLS	SNP	515	516	999	.	.	ID=k69_98089:SAMTOOLS:SNP:515;Variant_seq=G;Reference_seq=A;DP=4455;VDB=0.0378;AF1=0.4583;G3=0.08333,0.9167,1.498e-16;HWE=0.000926;AC1=11;DP4=952,817,1390,1120;MQ=33;FQ=999;PV4=0.32,0,0,1
+k69_98089	SAMTOOLS	SNP	522	523	999	.	.	ID=k69_98089:SAMTOOLS:SNP:522;Variant_seq=G;Reference_seq=A;DP=4698;VDB=0.0388;AF1=0.4168;G3=0.1656,0.8344,2.693e-36;HWE=0.00483;AC1=10;DP4=958,914,1327,1222;MQ=35;FQ=999;PV4=0.56,0,0,1
+k69_98089	SAMTOOLS	SNP	550	551	999	.	.	ID=k69_98089:SAMTOOLS:SNP:550;Variant_seq=A;Reference_seq=G;DP=4866;VDB=0.0385;AF1=0.5417;G3=2.024e-12,0.9167,0.08333;HWE=0.000926;AC1=13;DP4=1034,806,1547,1233;MQ=38;FQ=999;PV4=0.72,0,1e-231,1
+k69_98089	SAMTOOLS	SNP	625	626	999	.	.	ID=k69_98089:SAMTOOLS:SNP:625;Variant_seq=G;Reference_seq=A;DP=3557;VDB=0.0340;AF1=0.5;G3=8.721e-11,1,5.503e-15;HWE=4.53e-05;AC1=12;DP4=478,825,742,1369;MQ=41;FQ=999;PV4=0.38,0,2.7e-35,0.0059
+k69_98089	SAMTOOLS	SNP	693	694	999	.	.	ID=k69_98089:SAMTOOLS:SNP:693;Variant_seq=A;Reference_seq=T;DP=743;VDB=0.0038;AF1=0.5;G3=1.826e-14,1,3.643e-17;HWE=4.53e-05;AC1=12;DP4=37,238,66,367;MQ=39;FQ=999;PV4=0.58,6.3e-295,5.1e-12,1
+k69_98089	SAMTOOLS	SNP	717	718	999	.	.	ID=k69_98089:SAMTOOLS:SNP:717;Variant_seq=C;Reference_seq=T;DP=284;VDB=0.0010;AF1=0.5001;G3=2.555e-19,1,4.593e-12;HWE=4.54e-05;AC1=12;DP4=5,91,8,138;MQ=36;FQ=999;PV4=1,1.9e-90,2.7e-07,6.5e-05
+k69_98089	SAMTOOLS	SNP	723	724	999	.	.	ID=k69_98089:SAMTOOLS:SNP:723;Variant_seq=A;Reference_seq=G;DP=193;VDB=0.0010;AF1=0.4433;G3=0.08685,0.9132,1.287e-11;HWE=0.0015;AC1=11;DP4=5,79,5,45;MQ=37;FQ=999;PV4=0.5,2.9e-13,0.00011,0.47
+k69_98089	SAMTOOLS	SNP	726	727	999	.	.	ID=k69_98089:SAMTOOLS:SNP:726;Variant_seq=C;Reference_seq=T;DP=152;VDB=0.0008;AF1=0.4943;G3=0.0835,0.8466,0.06993;HWE=0.0149;AC1=12;DP4=4,49,5,32;MQ=36;FQ=999;PV4=0.48,5.3e-32,0.00016,0.43
diff -r be070a68521e -r b321e0517be3 umelt_service.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/umelt_service.py	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+
+##interrogate umelt service at Univ of Utah
+import sys
+import urllib
+import urllib2
+import xml.etree.ElementTree as ET
+import numpy as np
+import scipy as sp
+from scipy import interpolate
+from scipy.interpolate import interp1d
+
+
+url='https://www.dna.utah.edu/db/services/cgi-bin/udesign.cgi'
+timeout_sec=500 ## default for timeout
+
+# Query UW melt prediction service for a single sequence, returning default array for helicity, assuming within temperature range of 65-95
+def getmelt(input_seq):
+    values = {'seq' : input_seq, 'rs':0, 'dmso':0,'cation': 20 ,'mg': 2} # Note the buffer conditions
+    data = urllib.urlencode(values)
+    req = urllib2.Request(url, data)
+    try:
+        response = urllib2.urlopen(req,timeout=timeout_sec)
+    except urllib2.HTTPError, e:
+        print 'The server couldn\'t fulfill the request.'
+        print 'Error code: ', e.code
+    except urllib2.URLError, e:
+        print 'We failed to reach a server.'
+        print 'Reason: ', e.reason
+    else:
+        melt_data = response.read()
+        tree = ET.fromstring(melt_data)
+        helicity = [amp.find('helicity').text.split() for amp in tree.findall('amplicon')]
+        hels = np.array(helicity[0], dtype=np.float32).transpose() 
+        return hels
+
+# helicity[0] used because the default retreived data is a list of 3 lists (for WT, mu and hets). The 3 lists are identical for our data (no IUPAC) so only [0] is used.
+
+def getTm(hel_array):
+	temps=np.arange(65,100.5,0.5) # Temperature range of 65-100.5. Step of 0.5 NEEDS TO BE CHECKED..REcent change?
+	tck = interpolate.splrep(temps,hel_array,s=0)
+	xnew =np.arange(65,95.5,0.05)
+	yder = interpolate.splev(xnew,tck,der=1) # der=1, first derivative
+	return xnew[yder.argmin()] # Returns the x value corresponding to the minimum (peak) y value -> Tm
diff -r be070a68521e -r b321e0517be3 uniq.xml
--- a/uniq.xml	Thu Oct 18 19:47:07 2012 -0400
+++ b/uniq.xml	Thu May 22 20:30:19 2014 -0400
@@ -8,5 +8,3 @@
   <outputs>
      <data format="txt"  name="outputfile" />
   </outputs>
-
-</tool>
diff -r be070a68521e -r b321e0517be3 vcf2gvf.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcf2gvf.py	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,68 @@
+#!/usr/bin/env python
+"""
+Usage vcf2gvf.py <vcf_file input> <gff_file output>
+"""
+import sys,re
+
+##simplify the variant descriptor for GVF
+def get_vartype(type_str):
+    type_str=type_str.upper()
+    for V in ['COMPLEX', 'MNP', 'DEL', 'INDEL','INS','SNP']:
+        if V in type_str:
+            return V
+            break
+
+
+                                                                              
+in_vcf_file = open(sys.argv[1], 'r')
+out_gff_file = open(sys.argv[2], 'w')
+out_gff_file.write("#gff-version 3\n") ####gvf-version 1.06
+
+##only deal with tidy source lines, samtools is special needs
+source_pat = re.compile('##source=(\S+)', re.IGNORECASE)
+
+
+while True:
+    line=in_vcf_file.readline()
+    if line[0]!='#':
+        break
+    elif line[2:10]=='samtools':
+        source_type='SAMTOOLS'
+        break
+    else:
+        m=source_pat.match(line)
+        if m:
+            source_type=m.group(1).upper()
+            break
+
+
+##now read the data
+##samtools only distinguishes SNPs and indels
+##This is much complicated in highly heterozygous systems
+##see http://www.sequenceontology.org/miso/current_release/term/SO:0001059
+##GVF column 3 requires a type from this ontology
+###vcf type may be snp, mnp, ins, del, or complex.
+##for current purposes map multiple types to most complex state
+##ie SNP,SNP -> SNP; SNP,MNP-> MNP; SNP,complex 
+try:
+    for line in in_vcf_file:
+        if line[0] != '#':
+            var=line.split() ##see if var[7] has indel at start. If so add TYPE=INDEL for samtools case
+            info_field=var[7].split(';')
+            if info_field[0]=='INDEL':
+                info_field[0]="TYPE=INDEL"
+            info_dict=dict(X.split('=') for X in info_field)
+            ##if no TYPE key, then add TYPE=SNP for samtools case
+            if not info_dict.has_key('TYPE'):
+                info_dict['TYPE']='SNP';
+            var_type=get_vartype(info_dict['TYPE'])
+            ID=":".join([var[0],source_type,var_type,var[1]])
+            start=int(var[1])
+            length=len(var[3]) ## using reference length in this case
+            attributes=";".join(['ID='+ID,'Reference_seq='+var[3],'Variant_seq='+var[4]])
+            output_line=[var[0], source_type, var_type,  str(start), str(start+length-1) ,'.','.','.',attributes,"\n"]
+            out_gff_file.write("\t".join([str(X) for X in output_line]))
+finally:
+    in_vcf_file.close()
+    out_gff_file.close()
+
diff -r be070a68521e -r b321e0517be3 vcf2gvf.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcf2gvf.sh	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,47 @@
+#!/bin/sh
+##convert vcf to gvf
+##NOTE This is a very simple basic parser for a complex format.
+#It is intended for use with mpileup output where -g or -u flags are NOT used.
+
+##usage vcf2gvf.sh <vcf file> <outputfile>
+
+#Copyright 2012 John McCallum & Leshi Chen
+#New Zealand Institute for Plant and Food Research
+
+#New Zealand Institute for Plant and Food Research
+#This program is free software: you can redistribute it and/or modify
+#     it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+
+
+inputfile=$1
+outputfile=$2
+
+echo  "##gvf-version 1.05" > $outputfile
+
+awk '
+BEGIN {OFS="\t"}
+
+##get feature type 
+{if (index($8,"INDEL")== 1) {type="INDEL"} else {type="SNP"} }
+##get feature length
+{if (type=="SNP") 
+    {feat_length=1}
+    else {feat_length=length($4)} 
+}
+{end=($2+feat_length)}
+
+!/^#/  { print $1 ,"SAMTOOLS",type,$2,end,$6,".",".","ID="$1":SAMTOOLS:"type":"$2";Variant_seq="$5";Reference_seq="$4";"$8}
+
+END {print ""} 
+' "$inputfile" > "$outputfile"
\ No newline at end of file
diff -r be070a68521e -r b321e0517be3 vcf2gvf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcf2gvf.xml	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,58 @@
+<?xml version="1.0"?>
+<tool id="vcf2gvf_1" name="VCF to GFF3">
+  <description>convert vcf to gvf/gff3</description>
+  <command interpreter="bash">vcf2gvf.sh  $inputFile  $outputfile</command>
+  <inputs>
+    <param format="vcf" name="inputFile" type="data" label="Input vcf File" help="vcf file from mpileup" />
+  </inputs>
+  <outputs>
+<data format="gff3" name="outputfile" /> 
+
+  </outputs>
+<help>
+This tool provides a simple conversion from vcf to gvf.
+
+It is intended for use with Freebayes or with Samtools mpileup 
+
+Be sure to read the documentation to determine if it meets your requirements.
+
+* vcf documentation at http://samtools.sourceforge.net/samtools.shtml#6
+* GVF/GFF3 at http://www.sequenceontology.org/resources/gvf.html
+* Freebayes https://github.com/ekg/freebayes
+
+
+
+**input**
+
+::
+
+	PGSC0003DMB000000010	2042429	.	C	A	44.6	.	DP=10;VDB=0.0118;AF1=0.8295;AC1=7;DP4=2,1,3,4;MQ=20;FQ=8.78;PV4=1,5.2e-10,1,1	GT:PL:DP:GQ	0/1:14,0,42:5:23	1/1:27,6,0:2:9	1/1:15,3,0:1:7	1/1:30,6,0:2:9
+	PGSC0003DMB000000038	1756646	.	G	A	3.69	.	DP=15;VDB=0.0166;AF1=0.495;AC1=4;DP4=3,7,2,2;MQ=20;FQ=5.6;PV4=0.58,3.8e-09,1,0.31	GT:PL:DP:GQ	0/1:20,3,0:1:6	0/1:9,0,67:7:8	0/0:0,15,82:5:17	0/1:16,3,0:1:5
+	PGSC0003DMB000000064	1916664	.	T	C	8.12	.	DP=4;VDB=0.0151;AF1=1;AC1=8;DP4=0,0,0,3;MQ=20;FQ=-29.5	GT:PL:DP:GQ	1/1:14,3,0:1:5	1/1:0,0,0:0:3	1/1:13,3,0:1:5	1/1:15,3,0:1:5
+
+
+**output**
+
+
+::
+
+	PGSC0003DMB000000010	samtools	SNP	2042429	2042430	44.6	.	.	ID=PGSC0003DMB000000010:SAMTOOLS:SNP:2042429;Variant_seq=A;Reference_seq=C;DP=10;VDB=0.0118;AF1=0.8295;AC1=7;DP4=2,1,3,4;MQ=20;FQ=8.78;PV4=1,5.2e-10,1,1
+	PGSC0003DMB000000038	samtools	SNP	1756646	1756647	3.69	.	.	ID=PGSC0003DMB000000038:SAMTOOLS:SNP:1756646;Variant_seq=A;Reference_seq=G;DP=15;VDB=0.0166;AF1=0.495;AC1=4;DP4=3,7,2,2;MQ=20;FQ=5.6;PV4=0.58,3.8e-09,1,0.31
+	PGSC0003DMB000000064	samtools	SNP	1916664	1916665	8.12	.	.	ID=PGSC0003DMB000000064:SAMTOOLS:SNP:1916664;Variant_seq=C;Reference_seq=T;DP=4;VDB=0.0151;AF1=1;AC1=8;DP4=0,0,0,3;MQ=20;FQ=-29.5
+
+
+
+-----------------------
+
+*If you use this tool please cite:*
+
+A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data: 
+Application For  Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
+(2012)
+
+Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, 
+Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum
+
+
+</help>
+</tool>
diff -r be070a68521e -r b321e0517be3 vcf_gff.py
--- a/vcf_gff.py	Thu Oct 18 19:47:07 2012 -0400
+++ b/vcf_gff.py	Thu May 22 20:30:19 2014 -0400
@@ -46,6 +46,8 @@
         record_type = "SNP"
     for entry in rec:
         detail = entry.split("=")
+        if len(detail) < 2:
+            continue
         INFO[detail[0]] = detail[1]
     if INFO.has_key("DP"):
         reads = INFO.get("DP")
@@ -108,7 +110,9 @@
                 gen = "HET"
             if genotypes == "0/0":
                 gen = "HOM_ref"
-        else:
+        try: # set gen to 'NA' if still unset
+            gen
+        except NameError:
             gen = "NA"
         geno = ("%s:%s " % (reads, gen))
         genos += geno
@@ -141,11 +145,11 @@
             end = start 
         gen = get_gen(info[8:], reference)
         out_gff_file.write(
-            ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\tID=%s:%s:%d;Variant" +
+            ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\tID=%s:%s:%s:%d;Variant" +
              "_seq=%s;Reference_seq=%s;Total_reads=%s;Zygosity=%s\n") %
             ( seqid, source,record_type, start, end, score, strand, phase,seqid, 
-              record_type, start, variant, reference, reads, gen))
-    
+              source, record_type, start, variant, reference, reads, gen))
+
 out_gff_file.close()    
 
 
diff -r be070a68521e -r b321e0517be3 vcf_gff.xml
--- a/vcf_gff.xml	Thu Oct 18 19:47:07 2012 -0400
+++ b/vcf_gff.xml	Thu May 22 20:30:19 2014 -0400
@@ -8,6 +8,16 @@
   <outputs>
      <data format="gff3" name="outputfile" />
   </outputs>
+  <tests>
+        <test>
+                <param name="inputVcf" value="mpileup_out.vcf" ftype="vcf"/>
+                <output name="outputfile" file="mpileup_vcf_to_gff_output.gff"/>
+        </test>
+        <test>
+                <param name="inputVcf" value="freebayes_out.vcf" ftype="vcf"/>
+                <output name="outputfile" file="freebayes_vcf_to_gff_output.gff"/>
+        </test>
+  </tests>
 <help>
 
 ** Convert vcf to gff3**
@@ -58,4 +68,4 @@
 Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum
 
 </help>
-</tool>
\ No newline at end of file
+</tool>