Mercurial > repos > artbio > mutational_patterns
changeset 15:8182d1625433 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
author | artbio |
---|---|
date | Sun, 03 Oct 2021 09:29:04 +0000 |
parents | 56c8869a231e |
children | 31e7a33ecd71 |
files | mutational_patterns.R mutational_patterns.xml test-data/cosmic_output1.pdf test-data/cosmic_output2.pdf test-data/cosmic_output_v3.pdf test-data/denovo_1.RData test-data/denovo_output1.pdf test-data/sig_contrib_table.tsv test-data/sig_contrib_table_v3.tsv test-data/sigmatrix.tab test-data/spectrum_output1.pdf |
diffstat | 11 files changed, 205 insertions(+), 165 deletions(-) [+] |
line wrap: on
line diff
--- a/mutational_patterns.R Fri Jun 04 22:35:48 2021 +0000 +++ b/mutational_patterns.R Sun Oct 03 09:29:04 2021 +0000 @@ -184,7 +184,7 @@ rownames(nmf_res$contribution) <- paste0("NewSig_", 1:opt$newsignum) # Plot the 96-profile of the signatures: p5 <- plot_96_profile(nmf_res$signatures, condensed = TRUE) - new_sig_matrix <- reshape2::dcast(p5$data, substitution + context ~ variable, value.var = "value") + new_sig_matrix <- reshape2::dcast(p5$data, substitution + context ~ sample, value.var = "freq") new_sig_matrix <- format(new_sig_matrix, scientific = TRUE) write.table(new_sig_matrix, file = opt$sigmatrix, quote = FALSE, row.names = FALSE, sep = "\t") grid.arrange(p5) @@ -229,6 +229,7 @@ colnames(cancer_signatures) <- gsub("Signature.", "", colnames(cancer_signatures)) # shorten signature labels cosmic_tag <- "Signatures (Cosmic v2, March 2015)" cosmic_colors <- col_vector[1:30] + names(cosmic_colors) <- colnames(cancer_signatures) } else { sp_url <- "https://raw.githubusercontent.com/ARTbio/startbio/master/sigProfiler_SBS_signatures_2019_05_22.tsv" cancer_signatures <- read.table(sp_url, sep = "\t", header = TRUE) @@ -239,6 +240,7 @@ colnames(cancer_signatures) <- gsub("SBS", "", colnames(cancer_signatures)) # shorten signature labels cosmic_tag <- "Signatures (Cosmic v3, May 2019)" cosmic_colors <- col_vector[1:67] + names(cosmic_colors) <- colnames(cancer_signatures) } # Plot mutational profiles of the COSMIC signatures @@ -259,8 +261,9 @@ fit_res <- fit_to_signatures(pseudo_mut_mat, cancer_signatures) # Plot contribution barplots - pc3 <- plot_contribution(fit_res$contribution, cancer_signatures, coord_flip = T, mode = "absolute") - pc4 <- plot_contribution(fit_res$contribution, cancer_signatures, coord_flip = T, mode = "relative") + pc3 <- plot_contribution(fit_res$contribution, cancer_signatures, coord_flip = T, mode = "absolute") + pc4 <- plot_contribution(fit_res$contribution, cancer_signatures, coord_flip = T, mode = "relative") + if (is.na(opt$levels)[1]) { # if there are NO levels to display in graphs pc3_data <- pc3$data pc3 <- ggplot(pc3_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) + geom_bar(stat = "identity", position = "stack") + @@ -282,6 +285,7 @@ theme(panel.grid.minor.x = element_blank(), panel.grid.major.x = element_blank(), legend.position = "right", text = element_text(size = 8), axis.text.x = element_text(angle = 90, hjust = 1)) + } ##### # ggplot2 alternative if (!is.na(opt$levels)[1]) { # if there are levels to display in graphs @@ -342,7 +346,6 @@ } worklist <- as.data.frame(melt(worklist)) worklist[, 2] <- paste0(worklist[, 4], " - ", worklist[, 2]) - head(worklist) } colnames(worklist) <- c("signature", "sample", "value", "level") @@ -356,7 +359,7 @@ coord_polar("y", start = 0) + facet_wrap(.~sample) + labs(x = "", y = "Samples", fill = cosmic_tag) + scale_fill_manual(name = paste0(opt$signum, " most contributing\nsignatures\n(in each label/tissue)"), - values = cosmic_colors[as.numeric(levels(factor(worklist$label)))]) + + values = cosmic_colors[levels(worklist$signature)]) + theme(axis.text = element_blank(), axis.ticks = element_blank(), panel.grid = element_blank())
--- a/mutational_patterns.xml Fri Jun 04 22:35:48 2021 +0000 +++ b/mutational_patterns.xml Sun Oct 03 09:29:04 2021 +0000 @@ -1,13 +1,13 @@ -<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy14"> +<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy0"> <description>from genomic variations in vcf files</description> <requirements> - <requirement type="package" version="2.0.0=r40_0">bioconductor-mutationalpatterns</requirement> - <requirement type="package" version="1.6.6=r40h6115d3f_1">r-optparse</requirement> - <requirement type="package" version="0.2.20=r40h0357c0b_1002">r-rjson</requirement> - <requirement type="package" version="0.21.0=r40h0357c0b_1004">r-nmf</requirement> - <requirement type="package" version="2.3=r40h6115d3f_1003">r-gridextra</requirement> - <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement> - <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement> + <requirement type="package" version="3.2.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement> + <requirement type="package" version="1.6.6=r41hc72bb7e_1">r-optparse</requirement> + <requirement type="package" version="0.2.20=r41h03ef668_1002">r-rjson</requirement> + <requirement type="package" version="0.21.0=r41h03ef668_1004">r-nmf</requirement> + <requirement type="package" version="2.3=r41hc72bb7e_1003">r-gridextra</requirement> + <requirement type="package" version="1.4.3=r41hdfd78af_3">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement> + <requirement type="package" version="1.4.3=r41hdfd78af_3">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement> <!-- <requirement type="package" version="1.3.1000=r40_4">bioconductor-bsgenome.hsapiens.ncbi.grch38</requirement> <requirement type="package" version="0.99.1=r40_4">bioconductor-bsgenome.hsapiens.1000genomes.hs37d5</requirement> @@ -54,7 +54,7 @@ --cosmic_version '$set_cosmic.cosmic_version' --signum '$set_cosmic.signum' --output_cosmic $cosmic - #if $set_cosmic.contrib_matrix_out + #if $set_cosmic.contrib_matrix_out == 'yes' --sig_contrib_matrix $sig_contrib_matrix #end if #end if @@ -124,7 +124,7 @@ </conditional> <conditional name="set_cosmic"> - <param name="choices" type="select" label="Decompose with Cosmic signature v2" display="radio"> + <param name="choices" type="select" label="Decompose with Cosmic signatures" display="radio"> <option value="yes" selected="true">Yes</option> <option value="no">No</option> </param> @@ -136,8 +136,11 @@ <option value="v2" selected="true">Cosmic v2, March 2015</option> <option value="v3">Cosmic v3, May 2019</option> </param> - <param name="contrib_matrix_out" type="boolean" checked="false" label="Output Signature Contribution table ?" - help="Output the normalized signatures contributions for further visualization" /> + <param name="contrib_matrix_out" type="select" label="Output Signature Contribution table ?" + help="Output the normalized signatures contributions for further visualization" > + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> </when> <when value="no" /> </conditional> @@ -157,7 +160,7 @@ <filter>set_cosmic['choices'] == "yes"</filter> </data> <data name="sig_contrib_matrix" format="tabular" label="${tool.name}: Signature contribution table"> - <filter>set_cosmic['contrib_matrix_out']</filter> + <filter>set_cosmic['choices'] == "yes" and set_cosmic['contrib_matrix_out'] == "yes"</filter> </data> <data name="rdata" format="rdata" label="${tool.name}: RData file"> @@ -166,6 +169,82 @@ </outputs> <tests> + <!-- cosmic signatures with cosmic V3 --> + <test> + <param name="vcfs"> + <collection type="list"> + <element name="6" value="F.vcf"/> + <element name="7" value="G.vcf"/> + <element name="8" value="H.vcf"/> + <element name="9" value="I.vcf"/> + </collection> + </param> + <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/> + <param name="levels" value="FGHI_levels.tab" ftype="tabular"/> + <conditional name="set_spectrum"> + <param name="choices" value="no"/> + </conditional> + <conditional name="set_denovo"> + <param name="choices" value="no"/> + </conditional> + <conditional name="set_cosmic"> + <param name="choices" value="yes"/> + <param name="contrib_matrix_out" value="yes" /> + <param name="cosmic_version" value="v3"/> + </conditional> + <param name="signum" value="3" /> + <output name="cosmic" file="cosmic_output_v3.pdf" compare="sim_size"/> + <output name="sig_contrib_matrix" file="sig_contrib_table_v3.tsv" compare="sim_size"/> + </test> + + <!-- cosmic signatures --> + <test> + <param name="vcfs"> + <collection type="list"> + <element name="6" value="F.vcf"/> + <element name="7" value="G.vcf"/> + <element name="8" value="H.vcf"/> + <element name="9" value="I.vcf"/> + </collection> + </param> + <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/> + <param name="levels" value="FGHI_levels.tab" ftype="tabular"/> + <conditional name="set_spectrum"> + <param name="choices" value="no"/> + </conditional> + <conditional name="set_denovo"> + <param name="choices" value="no"/> + </conditional> + <conditional name="set_cosmic"> + <param name="choices" value="yes"/> + <param name="contrib_matrix_out" value="yes" /> + </conditional> + <param name="signum" value="3" /> + <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size"/> + <output name="sig_contrib_matrix" file="sig_contrib_table.tsv" compare="sim_size"/> + </test> + + <!-- cosmic signature on single sample --> + <test> + <param name="vcfs"> + <collection type="list"> + <element name="1" value="G.vcf"/> + </collection> + </param> + <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/> + <conditional name="set_spectrum"> + <param name="choices" value="no"/> + </conditional> + <conditional name="set_denovo"> + <param name="choices" value="no"/> + </conditional> + <conditional name="set_cosmic"> + <param name="choices" value="yes"/> + </conditional> + <param name="signum" value="5" /> + <output name="cosmic" file="cosmic_output2.pdf" compare="sim_size" delta="50000"/> + </test> + <!-- simple profile --> <test> <param name="vcfs"> @@ -219,53 +298,6 @@ <output name="sigmatrix" file="sigmatrix.tab" compare="sim_size"/> <output name="rdata" file="denovo_1.RData" compare="sim_size" delta="400000"/> <!-- delta="170000" --> </test> - - <!-- cosmic signatures --> - <test> - <param name="vcfs"> - <collection type="list"> - <element name="6" value="F.vcf"/> - <element name="7" value="G.vcf"/> - <element name="8" value="H.vcf"/> - <element name="9" value="I.vcf"/> - </collection> - </param> - <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/> - <param name="levels" value="FGHI_levels.tab" ftype="tabular"/> - <conditional name="set_spectrum"> - <param name="choices" value="no"/> - </conditional> - <conditional name="set_denovo"> - <param name="choices" value="no"/> - </conditional> - <conditional name="set_cosmic"> - <param name="choices" value="yes"/> - <param name="contrib_matrix_out" value="true" /> - </conditional> - <param name="signum" value="3" /> - <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size"/> - <output name="sig_contrib_matrix" file="sig_contrib_table.tsv" compare="sim_size"/> - </test> - <!-- cosmic signature on single sample --> - <test> - <param name="vcfs"> - <collection type="list"> - <element name="1" value="G.vcf"/> - </collection> - </param> - <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/> - <conditional name="set_spectrum"> - <param name="choices" value="no"/> - </conditional> - <conditional name="set_denovo"> - <param name="choices" value="no"/> - </conditional> - <conditional name="set_cosmic"> - <param name="choices" value="yes"/> - </conditional> - <param name="signum" value="5" /> - <output name="cosmic" file="cosmic_output2.pdf" compare="sim_size" delta="50000"/> - </test> </tests> <help>
--- a/test-data/sig_contrib_table.tsv Fri Jun 04 22:35:48 2021 +0000 +++ b/test-data/sig_contrib_table.tsv Sun Oct 03 09:29:04 2021 +0000 @@ -1,5 +1,5 @@ sample s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30 -ovary-I.vcf 0.110142906240717 0.0107179228940658 0.250337884546217 0 0.123574305205091 0.00064433123164414 0 0.132427942951795 0.0645286099734586 0 0.0449394465051191 0.0482562813691387 0.0021792135773442 0 0.0208527968750023 0.113202769843279 0 0 0 0 0 0 0 0 0.0534957402074307 0 0 0.0246998485796975 0 0 -ovary-H.vcf 0.105077406305297 0.0161426031811577 0.213744671485429 0 0.267847442499011 0 0 0.0744758833337775 0.0589788373729043 0 0.0260566297995198 0.00332317088253305 0.0101947253359771 0 0 0.165596602885273 0 0 0 0 0 0 0 0 0.0157724425494898 0 0.0064649564106814 0.0363246279589487 0 0 -lung-G.vcf 0.211033078587086 0.0166966912787851 0.172186940126079 0 0.286633042356631 0 0 0.00842344130070046 0.11400762247453 0 0.0288922172140213 0.0327352792025852 0 0 0 0.034128625357202 0 0 0.0288565039877324 0 0 0 0 0 0.0631355806535697 0 0.000844012191577089 0.00242696526950036 0 0 -lung-F.vcf 0.275881644071761 0.00660164806875313 0.17426347088712 0 0.102714094410494 0 0 0.0917555941611345 0.0202950075653247 0 0.0296908924905143 0.0090315352239272 0 0 0 0.188940992761965 0 0 0 0 0 0 0 0 0.0273695319074987 0 0.00555599996394483 0.0404508145574958 0 0.0274487739300663 +ovary-I.vcf 0.11366483685008 0.0109938593266657 0.261053482791866 0 0.102195880307416 0.00220769920517984 0 0.121596331607151 0.0667024002680757 0 0.0463559883343337 0.0477514837858505 0.00153570456409855 0 0.0196723565031216 0.125168078635871 0 0 0 0 0 0 0 0 0.056462960047836 0 0.000124367513387182 0.0245145702590675 0 0 +ovary-H.vcf 0.108363933620392 0.0163896275457592 0.219669872246722 0 0.267579919199733 0 0 0.0644683944374041 0.0647530723986353 0 0.0255690291284295 0 0.0096156971999939 0 0 0.16879742588098 0 0 0 0 0 0 0 0 0.0144022954450145 0 0.00628915179499457 0.0341015811019413 0 0 +lung-G.vcf 0.216042386729494 0.0163285606624902 0.174782553623772 0 0.243519493008331 0 0 0.00859703357366864 0.122147877946073 0 0.031028717517658 0.0398485713623127 0 0 0 0.0426507272713916 0 0 0.0331593375475991 0 0 0 0 0 0.0690376730723399 0 0.00121112083973226 0.00164594684513809 0 0 +lung-F.vcf 0.277447721812717 0.00581547878718051 0.177348626019748 0 0.1009356992577 0 0 0.0920458551898083 0.0183096024827367 0 0.0300240298284301 0.00396441475927008 0 0 0 0.195845126035802 0 0 0 0 0 0 0 0 0.0270963890910293 0 0.0049085436021671 0.041321577314175 0 0.0249369358192356
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sig_contrib_table_v3.tsv Sun Oct 03 09:29:04 2021 +0000 @@ -0,0 +1,5 @@ +sample s1 s2 s3 s4 s5 s6 s7a s7b s7c s7d s8 s9 s10a s10b s11 s12 s13 s14 s15 s16 s17a s17b s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30 s31 s32 s33 s34 s35 s36 s37 s38 s39 s40 s41 s42 s43 s44 s45 s46 s47 s48 s49 s50 s51 s52 s53 s54 s55 s56 s57 s58 s59 s60 s84 s85 +ovary-I.vcf 0.0292102144556227 0 0 0.00144007322742414 0 0.0504390788292217 0.00194348408726673 0 0.0525707708741538 0 0.0914724303738797 0 0.000832163233383592 0 0 0 0.00842487825711237 0 0.0135094432679645 0.0366586044772389 0 0 0.0185740536261001 0.00229375063200434 0 0.00970266938170121 0 0 0.00599759333539559 0.0421114673613094 0.0114310779471638 0 0.0135490307866796 0 0.0296793772659665 0.0277524342410843 0.0454269664537971 0.00938724128600892 0.0136144947369238 0 0 0.0833465920869942 0 0.137690178135469 0 0 0 0.00953146514960113 0.0202102619863343 0 0 0 0 4.88486910392704e-05 0.00760389505513268 0.0232276886439185 0 0 0.013878903464201 0 0 0.058642750046278 0.129529443690174 0.000268674913454976 0 0 0 +ovary-H.vcf 0.0523809674402057 0 0 0.0073487755957751 0 0 0.00289534105048845 0 0.028141106223541 0.00357241172591758 0.0900610723552876 0 0.00471257812773401 0 0 0 0.0152354080005807 0 0 0.056026125482423 0 0.00257191790029753 0 0.0165305233542475 0 0.000141899985605957 0 0 0.00488001259024111 0.00918859610852697 0.00475106755263085 0.00663010539344573 0.017109685037444 0 0.04731550745362 0.00365691117000763 0.0328768691449399 0.0120314432988265 0.0167811048132417 0 0 0.0950039544413254 0 0.137196255594851 0 0 0 0 0.0597953621090927 0 0 0 0 4.23604750551013e-05 0.0121309998776711 0.00973226374395621 0 0.00222509583262053 0.0251951439030708 0.0118558225702647 0 0.0846395405044328 0.125310604958315 0.00203316618431609 0 0 0 +lung-G.vcf 0.0873029632099988 0 0 0 0 0.0479104551341112 0.00776867305403075 0 0.0313814579173264 0 0.0609850595672004 0.0172622613117254 0 0.00012666179996385 0 0 0.00765587561722924 0 0 0.0278690467140333 0.000454577309760022 0 0.0206812596225624 0.0359443715017539 0 0.0120875070366763 0.00187879472330278 0 0.00683351257522683 0.0494238708587332 0 0 0 0 0.0480909479022159 0.00328524460204372 0.037243337279276 0.000684746817696913 0.0170460736503824 0 0 0.120242044269861 0 0.0912990485885233 0 0 0.00198825222515588 0 0.00367924369018231 0 0 0.00127107492891469 0 0 0 0.0337265499103692 0 0.00040976068762453 0.035143574313439 0 0 0.080043690949342 0.096390826001613 0 0.00205878889713283 0.0118304473325925 0 +lung-F.vcf 0.130972951527932 0 0.0761687896979774 0 0 0 0 0 0.0340317364900266 0 0.0786848101409268 0 0.00232431375487017 0.00924283426133058 0 0 0 0 0 0.0454990529437777 0 0 0.0111440674145277 0.0156984823484767 0 0.00368064004289289 0.00101383322501298 0 0.00769126266914517 0.0114608643279846 0 0.000168984385199036 0.0236023336834282 0 0.064421387701359 0.00659674935231646 0.036711297327122 0.00568327050616103 0.00956407247236277 0 0 0.0874117950073058 0 0.0752825647107504 0 0 0 0.00313252048097358 0.0213677245928594 0 0 0.0221471177980541 0 0.000825664351643732 0 0.0132117228813227 0 0.00204298080257053 0.0390511638798427 0 0 0.0245617897055234 0.122391156939586 0.00304240662816143 0 0.0111696579485762 0
--- a/test-data/sigmatrix.tab Fri Jun 04 22:35:48 2021 +0000 +++ b/test-data/sigmatrix.tab Sun Oct 03 09:29:04 2021 +0000 @@ -1,97 +1,97 @@ substitution context NewSig_1 NewSig_2 NewSig_3 NewSig_4 -C>A A.A 2.012349e-02 2.099063e-02 1.788529e-02 2.529973e-02 -C>A A.C 1.232623e-02 5.099845e-05 2.019020e-02 8.344265e-03 -C>A A.G 2.056317e-03 5.061512e-03 5.110667e-03 5.598599e-04 -C>A A.T 4.276274e-03 7.030586e-03 1.433976e-02 9.044799e-03 -C>A C.A 9.858499e-03 6.774294e-03 1.254817e-02 1.109854e-02 -C>A C.C 7.182083e-03 5.137412e-03 1.754580e-02 7.871756e-03 -C>A C.G 3.071657e-03 7.744685e-04 3.478215e-03 3.033573e-03 -C>A C.T 9.805120e-04 1.022892e-02 8.612445e-03 1.089991e-02 -C>A G.A 1.295094e-02 5.191677e-03 2.838657e-03 1.229298e-02 -C>A G.C 4.262714e-03 5.183579e-03 8.941540e-03 5.390685e-03 -C>A G.G 3.769228e-03 1.557726e-03 1.699600e-03 3.945304e-03 -C>A G.T 6.573060e-03 1.031818e-04 1.059791e-02 7.185424e-03 -C>A T.A 3.862713e-03 1.624881e-02 5.519485e-03 1.246359e-02 -C>A T.C 8.824563e-03 6.792814e-03 4.042968e-03 1.212436e-02 -C>A T.G 1.024188e-03 9.815808e-04 2.029646e-03 1.087012e-03 -C>A T.T 1.181704e-02 9.618044e-03 1.665114e-02 1.307952e-02 -C>G A.A 1.983228e-02 1.270519e-02 1.655687e-02 1.398506e-02 -C>G A.C 4.742892e-11 1.043116e-02 9.102239e-03 2.314023e-20 -C>G A.G 2.906055e-03 1.687383e-03 5.265593e-03 2.218107e-03 -C>G A.T 6.407465e-03 8.581278e-03 1.079483e-02 9.668306e-03 -C>G C.A 3.411641e-03 6.888991e-03 7.212837e-03 7.949635e-03 -C>G C.C 1.962245e-04 9.715947e-03 1.158418e-12 7.156965e-03 -C>G C.G 3.300401e-20 1.855024e-03 4.346525e-03 6.200559e-03 -C>G C.T 9.865314e-03 1.922285e-03 6.273441e-03 6.226190e-03 -C>G G.A 1.351834e-19 2.119713e-03 1.072168e-02 8.229779e-03 -C>G G.C 2.379848e-03 4.610717e-03 8.965747e-04 6.505033e-03 -C>G G.G 6.979718e-04 1.181697e-03 4.111756e-03 2.523959e-03 -C>G G.T 2.220903e-03 5.934769e-03 8.611327e-03 6.739344e-03 -C>G T.A 3.709345e-03 8.786940e-03 7.620791e-03 8.983741e-03 -C>G T.C 3.827093e-03 8.865683e-03 6.057793e-03 6.240498e-03 -C>G T.G 1.899263e-04 4.938065e-03 3.040335e-03 1.626378e-03 -C>G T.T 3.860261e-03 2.446381e-02 2.353559e-02 1.511199e-02 -C>T A.A 3.499419e-02 3.714546e-02 4.085734e-02 3.151538e-02 -C>T A.C 1.719840e-02 1.389005e-02 5.154001e-03 1.603745e-02 -C>T A.G 7.482535e-02 1.348050e-02 3.052063e-02 1.592390e-02 -C>T A.T 1.607143e-02 1.438585e-02 1.967215e-02 1.741898e-02 -C>T C.A 1.606874e-02 1.435234e-02 1.105389e-02 1.125796e-02 -C>T C.C 1.700219e-02 9.214402e-03 1.282668e-02 1.377429e-02 -C>T C.G 4.356691e-02 1.624586e-02 1.169686e-02 1.963077e-02 -C>T C.T 2.301602e-02 3.266347e-02 1.574218e-02 2.039183e-02 -C>T G.A 1.970589e-02 7.742080e-03 1.178227e-02 1.297792e-02 -C>T G.C 1.466426e-02 1.914382e-02 6.909098e-03 1.355502e-02 -C>T G.G 3.701827e-02 2.542796e-02 1.262381e-02 3.190790e-02 -C>T G.T 1.382222e-02 2.392818e-02 6.174897e-03 1.508942e-02 -C>T T.A 1.143013e-02 1.914536e-02 1.002998e-02 7.458921e-03 -C>T T.C 1.879514e-02 2.009898e-02 1.421423e-02 1.556176e-02 -C>T T.G 3.061491e-02 4.743450e-03 1.167740e-02 7.144683e-03 -C>T T.T 3.133938e-02 2.219653e-02 3.807693e-02 3.192865e-02 -T>A A.A 1.841481e-02 8.914346e-03 1.741295e-02 1.361688e-02 -T>A A.C 3.425691e-03 8.698638e-03 3.992626e-03 5.443164e-03 -T>A A.G 9.072656e-03 1.149533e-02 1.354019e-03 8.223373e-03 -T>A A.T 9.659453e-03 1.830189e-02 1.174139e-02 1.710128e-02 -T>A C.A 2.727069e-03 7.915424e-03 5.772823e-03 4.530720e-03 -T>A C.C 1.215316e-02 3.470147e-03 7.886743e-03 1.369393e-02 -T>A C.G 3.791221e-03 6.605963e-03 3.294232e-03 8.818173e-03 -T>A C.T 6.289729e-03 1.435186e-02 3.597548e-03 1.211551e-02 -T>A G.A 6.615841e-04 4.146662e-03 4.933783e-03 4.863214e-03 -T>A G.C 1.515807e-03 4.210462e-03 3.382936e-03 9.183128e-04 -T>A G.G 1.070023e-02 1.089710e-02 5.492536e-03 8.802992e-03 -T>A G.T 8.128051e-03 4.233917e-03 9.103699e-03 1.259684e-02 -T>A T.A 1.476324e-02 6.549494e-03 1.579044e-02 7.620545e-03 -T>A T.C 6.738527e-03 8.767946e-04 7.353978e-03 5.436410e-03 -T>A T.G 2.186518e-03 5.445354e-03 2.568144e-03 7.932364e-03 -T>A T.T 1.942541e-02 1.590353e-02 2.306069e-02 3.009347e-02 -T>C A.A 3.011297e-02 3.375076e-02 4.906885e-02 3.383597e-02 -T>C A.C 9.041893e-03 8.933211e-03 8.243474e-03 6.303632e-03 -T>C A.G 2.247578e-02 9.001629e-03 1.950973e-02 8.972544e-03 -T>C A.T 1.210116e-02 1.578255e-02 1.360358e-02 9.528566e-03 -T>C C.A 6.835997e-03 6.652934e-03 1.036887e-02 7.994706e-03 -T>C C.C 9.462334e-03 6.392714e-03 8.437885e-03 1.653238e-02 -T>C C.G 7.156018e-03 1.612832e-02 1.225799e-02 9.579249e-03 -T>C C.T 1.040136e-02 2.530647e-02 1.208573e-02 1.371705e-02 -T>C G.A 8.743261e-03 1.074754e-02 5.087249e-03 1.090594e-02 -T>C G.C 6.111817e-03 6.456267e-03 3.668932e-20 6.346677e-03 -T>C G.G 1.768834e-02 1.377477e-02 1.512171e-02 1.240640e-02 -T>C G.T 3.605052e-03 1.397132e-02 1.282818e-02 1.036663e-02 -T>C T.A 5.577357e-03 1.122841e-02 7.516272e-03 9.852123e-03 -T>C T.C 2.142753e-02 1.003311e-02 1.311934e-02 1.883301e-02 -T>C T.G 3.231084e-03 7.639140e-03 1.374439e-02 6.010940e-03 -T>C T.T 1.771125e-02 5.247659e-02 2.430165e-02 3.016747e-02 -T>G A.A 1.331124e-02 1.426333e-02 7.805243e-05 7.473665e-03 -T>G A.C 3.887921e-03 1.684454e-03 1.435130e-04 6.445063e-04 -T>G A.G 2.394241e-03 5.040173e-03 6.853239e-03 6.994037e-03 -T>G A.T 6.066623e-03 7.374853e-03 2.079215e-10 5.136694e-03 -T>G C.A 5.000218e-10 8.218020e-03 3.668932e-20 2.314023e-20 -T>G C.C 3.300401e-20 1.904378e-03 4.043369e-03 4.672135e-03 -T>G C.G 4.310666e-03 2.256883e-03 8.181657e-03 1.928646e-03 -T>G C.T 2.128603e-03 9.425709e-04 8.787753e-03 6.815812e-04 -T>G G.A 2.012235e-03 4.628783e-04 4.459546e-03 1.814827e-03 -T>G G.C 3.997247e-03 1.335924e-03 1.270853e-03 3.568581e-03 -T>G G.G 7.790802e-03 1.175435e-02 8.700500e-03 8.985015e-03 -T>G G.T 6.538479e-03 1.329525e-02 4.903674e-03 1.074729e-02 -T>G T.A 2.781217e-03 4.774228e-03 2.965653e-03 7.301491e-03 -T>G T.C 5.182071e-03 5.200467e-03 5.617300e-03 2.629881e-03 -T>G T.G 5.245736e-03 1.345072e-02 1.698469e-02 9.832179e-03 -T>G T.T 2.041928e-02 1.752970e-02 3.978473e-02 1.976735e-02 +C>A A.A 1.856821e-02 2.482023e-02 1.879304e-02 2.144868e-02 +C>A A.C 1.985096e-02 8.856811e-03 4.176376e-03 7.275623e-03 +C>A A.G 4.613707e-03 1.032560e-03 7.399596e-03 1.283205e-03 +C>A A.T 1.077097e-02 1.152945e-02 1.110411e-02 3.506614e-03 +C>A C.A 1.234686e-02 1.058479e-02 7.778853e-03 8.511073e-03 +C>A C.C 1.527507e-02 9.706857e-03 1.091358e-02 3.977471e-03 +C>A C.G 3.595068e-03 3.053798e-03 1.065706e-03 2.488491e-03 +C>A C.T 4.654944e-03 1.331055e-02 1.146678e-02 3.015206e-03 +C>A G.A 5.984606e-03 9.241989e-03 1.639336e-13 1.380331e-02 +C>A G.C 7.683094e-03 6.339795e-03 8.137271e-03 3.391593e-03 +C>A G.G 2.406023e-03 3.640987e-03 1.456895e-04 3.942915e-03 +C>A G.T 1.020608e-02 7.739365e-03 2.399885e-03 4.235560e-03 +C>A T.A 3.961933e-03 1.275900e-02 1.466472e-02 6.814391e-03 +C>A T.C 5.337093e-03 1.162648e-02 9.105310e-04 1.013653e-02 +C>A T.G 1.877937e-03 6.162730e-04 1.878461e-03 6.682628e-04 +C>A T.T 1.560352e-02 1.326934e-02 1.247051e-02 9.445224e-03 +C>G A.A 1.972775e-02 1.228149e-02 1.195633e-02 1.727448e-02 +C>G A.C 5.836059e-03 1.655810e-03 1.694621e-02 9.062109e-07 +C>G A.G 5.200216e-03 2.559643e-03 3.166565e-03 1.532897e-03 +C>G A.T 9.324164e-03 1.095739e-02 1.081958e-02 6.258396e-03 +C>G C.A 5.617809e-03 9.345902e-03 8.284139e-03 3.880938e-03 +C>G C.C 3.534086e-20 8.210895e-03 7.727184e-03 2.254830e-03 +C>G C.G 2.262327e-03 7.340603e-03 3.022013e-03 9.156563e-05 +C>G C.T 8.224646e-03 5.017294e-03 7.003901e-04 8.665738e-03 +C>G G.A 6.954941e-03 1.139806e-02 4.622361e-03 3.514270e-20 +C>G G.C 7.064656e-04 6.998058e-03 2.537477e-03 3.965493e-03 +C>G G.G 3.080436e-03 3.328074e-03 2.929015e-03 1.461945e-04 +C>G G.T 6.360999e-03 8.512373e-03 9.008932e-03 2.005772e-03 +C>G T.A 5.553775e-03 1.062558e-02 9.424149e-03 4.924035e-03 +C>G T.C 5.248185e-03 7.233109e-03 9.634964e-03 4.359934e-03 +C>G T.G 1.845306e-03 2.417185e-03 6.595859e-03 6.782687e-04 +C>G T.T 1.587889e-02 2.049222e-02 3.439640e-02 5.050564e-03 +C>T A.A 3.911250e-02 3.225079e-02 4.206848e-02 3.385188e-02 +C>T A.C 8.757053e-03 1.352629e-02 6.991724e-03 1.974727e-02 +C>T A.G 5.231138e-02 1.925044e-07 3.026394e-03 6.399169e-02 +C>T A.T 1.874677e-02 1.836710e-02 1.620182e-02 1.541248e-02 +C>T C.A 1.408680e-02 9.572305e-03 1.224985e-02 1.529038e-02 +C>T C.C 1.412526e-02 1.293054e-02 7.720717e-03 1.618405e-02 +C>T C.G 2.458679e-02 1.097265e-02 2.704009e-03 4.320455e-02 +C>T C.T 1.682814e-02 1.962601e-02 2.870932e-02 2.757164e-02 +C>T G.A 1.501424e-02 1.146890e-02 4.373561e-03 1.710170e-02 +C>T G.C 8.581633e-03 1.197143e-02 1.469853e-02 1.798870e-02 +C>T G.G 2.050911e-02 2.694316e-02 1.193358e-02 4.080066e-02 +C>T G.T 6.725450e-03 1.485333e-02 2.022066e-02 1.821305e-02 +C>T T.A 9.790349e-03 7.433059e-03 1.994759e-02 1.263779e-02 +C>T T.C 1.594645e-02 1.460332e-02 1.802766e-02 1.886875e-02 +C>T T.G 2.019449e-02 4.552012e-04 8.162605e-12 2.690217e-02 +C>T T.T 3.604766e-02 3.365274e-02 2.789390e-02 2.769743e-02 +T>A A.A 1.765667e-02 1.321109e-02 1.065894e-02 1.583119e-02 +T>A A.C 1.820098e-03 5.510611e-03 8.183147e-03 4.599082e-03 +T>A A.G 4.665541e-03 6.215514e-03 6.135328e-03 1.001896e-02 +T>A A.T 9.785657e-03 1.833578e-02 1.768249e-02 1.248205e-02 +T>A C.A 4.242335e-03 5.517088e-03 9.041105e-03 3.634763e-03 +T>A C.C 8.948010e-03 1.166917e-02 2.179799e-05 1.148913e-02 +T>A C.G 2.492456e-03 9.694116e-03 4.293775e-03 5.700343e-03 +T>A C.T 2.882218e-03 1.297743e-02 1.071267e-02 1.009712e-02 +T>A G.A 3.223737e-03 6.245735e-03 5.842451e-03 9.200857e-04 +T>A G.C 2.805377e-03 1.213230e-03 5.828460e-03 1.503090e-03 +T>A G.G 6.898206e-03 7.300718e-03 8.003532e-03 1.222177e-02 +T>A G.T 9.120314e-03 1.347850e-02 3.249901e-03 7.453304e-03 +T>A T.A 1.622536e-02 6.931133e-03 9.627554e-03 1.174564e-02 +T>A T.C 6.760912e-03 5.595476e-03 9.698282e-04 5.499357e-03 +T>A T.G 1.866485e-03 8.652201e-03 2.256983e-03 3.519494e-03 +T>A T.T 2.145214e-02 3.177788e-02 1.505847e-02 1.981508e-02 +T>C A.A 4.427759e-02 3.786828e-02 4.544423e-02 2.650778e-02 +T>C A.C 8.998306e-03 4.599474e-03 1.004905e-02 8.722935e-03 +T>C A.G 2.243087e-02 6.118842e-03 1.134205e-02 1.802892e-02 +T>C A.T 1.373384e-02 9.886587e-03 1.685322e-02 1.176445e-02 +T>C C.A 8.656233e-03 9.072748e-03 8.862799e-03 6.112781e-03 +T>C C.C 8.714585e-03 1.690442e-02 3.565029e-03 9.871972e-03 +T>C C.G 1.071206e-02 1.004291e-02 1.850434e-02 7.540034e-03 +T>C C.T 1.017263e-02 1.448259e-02 2.608108e-02 1.403170e-02 +T>C G.A 5.126616e-03 1.108508e-02 8.768450e-03 1.036693e-02 +T>C G.C 5.204634e-12 5.747845e-03 3.143501e-03 8.849255e-03 +T>C G.G 1.669831e-02 1.133208e-02 1.267705e-02 1.603702e-02 +T>C G.T 8.671437e-03 1.325475e-02 1.721725e-02 5.039773e-03 +T>C T.A 6.260030e-03 1.102551e-02 1.167533e-02 7.016389e-03 +T>C T.C 1.517718e-02 1.699912e-02 6.470473e-03 2.077129e-02 +T>C T.G 9.336917e-03 8.764205e-03 1.160437e-02 2.331889e-03 +T>C T.T 1.903513e-02 3.432098e-02 5.540849e-02 2.562376e-02 +T>G A.A 3.993541e-03 4.978625e-03 8.356632e-03 1.578506e-02 +T>G A.C 1.728186e-03 3.099935e-20 6.777648e-15 3.511484e-03 +T>G A.G 5.502959e-03 8.711266e-03 5.367147e-03 2.059172e-03 +T>G A.T 1.499753e-03 4.210842e-03 3.978567e-03 7.977656e-03 +T>G C.A 3.534086e-20 4.234149e-16 8.909125e-03 1.246735e-03 +T>G C.C 1.909719e-03 6.194908e-03 2.037866e-03 5.448839e-04 +T>G C.G 7.443573e-03 2.206694e-03 4.942085e-03 2.758675e-03 +T>G C.T 7.417469e-03 1.454301e-03 5.521245e-03 5.632697e-19 +T>G G.A 4.032749e-03 2.126988e-03 2.146375e-03 9.845592e-04 +T>G G.C 2.308308e-03 3.091434e-03 3.322218e-20 3.632777e-03 +T>G G.G 8.852942e-03 9.064804e-03 1.199615e-02 7.843944e-03 +T>G G.T 4.276432e-03 1.084606e-02 1.101937e-02 9.425060e-03 +T>G T.A 2.351390e-03 8.100255e-03 3.683601e-03 3.923489e-03 +T>G T.C 5.580464e-03 2.444033e-03 5.806015e-03 5.018502e-03 +T>G T.G 1.287955e-02 1.265933e-02 1.969184e-02 4.871262e-03 +T>G T.T 3.545360e-02 2.295036e-02 2.946636e-02 1.477102e-02