diff test-data/chrMT-PE-VCF-BAM-genMutModel.p @ 0:6e75a84e9338 draft

planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
author thondeboer
date Tue, 15 May 2018 02:39:53 -0400
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chrMT-PE-VCF-BAM-genMutModel.p	Tue May 15 02:39:53 2018 -0400
@@ -0,0 +1,1401 @@
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+s(g309
+S'GAC'
+p520
+tp521
+F0.0
+s(S'CAG'
+p522
+S'CGG'
+p523
+tp524
+F1.0
+s(g325
+S'TTC'
+p525
+tp526
+F0.0
+s(g161
+S'ACT'
+p527
+tp528
+F0.0
+s(g130
+S'TGA'
+p529
+tp530
+F0.0
+s(g409
+S'CAC'
+p531
+tp532
+F0.0
+s(g220
+S'GGA'
+p533
+tp534
+F0.0
+s(g197
+S'TAG'
+p535
+tp536
+F0.0
+s(g361
+S'TTG'
+p537
+tp538
+F0.0
+s(S'AGG'
+p539
+S'AAG'
+p540
+tp541
+F1.0
+s(g284
+S'TGC'
+p542
+tp543
+F0.0
+s(g462
+S'CCG'
+p544
+tp545
+F0.0
+s(g346
+S'GAG'
+p546
+tp547
+F0.0
+s(g339
+S'ACC'
+p548
+tp549
+F0.0
+s(g431
+S'CGG'
+p550
+tp551
+F0.0
+s(g315
+S'CGA'
+p552
+tp553
+F0.0
+s(g392
+S'GTA'
+p554
+tp555
+F0.0
+s(g139
+S'AAG'
+p556
+tp557
+F0.0
+s(g438
+S'GAT'
+p558
+tp559
+F0.0
+s(g258
+S'TTC'
+p560
+tp561
+F0.0
+s(g191
+S'TAG'
+p562
+tp563
+F0.0
+s(g161
+S'ATT'
+p564
+tp565
+F0.0
+s(g379
+S'GGC'
+p566
+tp567
+F0.0
+s(g287
+S'CGC'
+p568
+tp569
+F0.0
+s(g462
+S'CTG'
+p570
+tp571
+F0.0
+s(g366
+S'TCT'
+p572
+tp573
+F0.0
+s(g144
+S'ACG'
+p574
+tp575
+F0.0
+s(g312
+S'CAC'
+p576
+tp577
+F0.0
+s(g438
+S'GTT'
+p578
+tp579
+F0.0
+s(g284
+S'TAC'
+p580
+tp581
+F0.0
+s(g203
+S'GCG'
+p582
+tp583
+F0.0
+s(g226
+S'GAA'
+p584
+tp585
+F0.0
+s(g229
+S'CTG'
+p586
+tp587
+F0.0
+s(g299
+S'CAA'
+p588
+tp589
+F0.0
+ssS'AVG_MUT_RATE'
+p590
+F0.0009053597295992274
+sS'INDEL_FREQ'
+p591
+(dp592
+I1
+F1.0000000000000002
+ss.
\ No newline at end of file