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changeset 15:8182d1625433 draft

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"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>
 
Binary file test-data/cosmic_output1.pdf has changed
Binary file test-data/cosmic_output2.pdf has changed
Binary file test-data/cosmic_output_v3.pdf has changed
Binary file test-data/denovo_1.RData has changed
Binary file test-data/denovo_output1.pdf has changed
--- 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
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