From 6d8d24ed070d02718da9cb35aaa7eaa59358ea6b Mon Sep 17 00:00:00 2001 From: Tim Fennell Date: Sun, 3 May 2026 08:41:06 -0600 Subject: [PATCH] Add test fixtures for the riker module Adds example outputs from the six riker subtools that the new MultiQC module parses (alignment, basic, gcbias, hybcap, isize, wgs). Files are generated from public 1000G data (HG00240 exome capture; HG03953 WGS) using riker against the parallel PR that adds a `sample` column to every output (fulcrumgenomics/riker#21). Companion to the MultiQC PR adding the riker module. --- .../alignment/HG00240.alignment-metrics.txt | 4 + .../alignment/HG03953.alignment-metrics.txt | 4 + .../HG00240.base-distribution-by-cycle.txt | 201 +++ .../basic/HG00240.mean-quality-by-cycle.txt | 201 +++ .../HG00240.quality-score-distribution.txt | 8 + .../HG03953.base-distribution-by-cycle.txt | 301 +++++ .../basic/HG03953.mean-quality-by-cycle.txt | 301 +++++ .../HG03953.quality-score-distribution.txt | 8 + .../riker/gcbias/HG03953.gcbias-detail.txt | 102 ++ .../riker/gcbias/HG03953.gcbias-summary.txt | 2 + .../riker/hybcap/HG00240.hybcap-metrics.txt | 2 + .../riker/isize/HG00240.isize-histogram.txt | 742 +++++++++++ .../riker/isize/HG00240.isize-metrics.txt | 2 + .../riker/isize/HG03953.isize-histogram.txt | 1087 +++++++++++++++++ .../riker/isize/HG03953.isize-metrics.txt | 2 + .../riker/wgs/HG03953.wgs-coverage.txt | 252 ++++ .../modules/riker/wgs/HG03953.wgs-metrics.txt | 2 + 17 files changed, 3221 insertions(+) create mode 100644 data/modules/riker/alignment/HG00240.alignment-metrics.txt create mode 100644 data/modules/riker/alignment/HG03953.alignment-metrics.txt create mode 100644 data/modules/riker/basic/HG00240.base-distribution-by-cycle.txt create mode 100644 data/modules/riker/basic/HG00240.mean-quality-by-cycle.txt create mode 100644 data/modules/riker/basic/HG00240.quality-score-distribution.txt create mode 100644 data/modules/riker/basic/HG03953.base-distribution-by-cycle.txt create mode 100644 data/modules/riker/basic/HG03953.mean-quality-by-cycle.txt create mode 100644 data/modules/riker/basic/HG03953.quality-score-distribution.txt create mode 100644 data/modules/riker/gcbias/HG03953.gcbias-detail.txt create mode 100644 data/modules/riker/gcbias/HG03953.gcbias-summary.txt create mode 100644 data/modules/riker/hybcap/HG00240.hybcap-metrics.txt create mode 100644 data/modules/riker/isize/HG00240.isize-histogram.txt create mode 100644 data/modules/riker/isize/HG00240.isize-metrics.txt create mode 100644 data/modules/riker/isize/HG03953.isize-histogram.txt create mode 100644 data/modules/riker/isize/HG03953.isize-metrics.txt create mode 100644 data/modules/riker/wgs/HG03953.wgs-coverage.txt create mode 100644 data/modules/riker/wgs/HG03953.wgs-metrics.txt diff --git a/data/modules/riker/alignment/HG00240.alignment-metrics.txt b/data/modules/riker/alignment/HG00240.alignment-metrics.txt new file mode 100644 index 00000000..b61a2d25 --- /dev/null +++ b/data/modules/riker/alignment/HG00240.alignment-metrics.txt @@ -0,0 +1,4 @@ +sample category total_reads aligned_reads frac_aligned hq_aligned_reads hq_aligned_bases hq_aligned_q20_bases hq_median_mismatches mismatch_rate hq_mismatch_rate indel_rate mean_read_length sd_read_length median_read_length mad_read_length min_read_length max_read_length mean_aligned_read_length aligned_reads_in_pairs frac_aligned_in_pairs reads_improperly_paired frac_reads_improperly_paired bad_cycles strand_balance frac_chimeras frac_softclipped_reads frac_hardclipped_reads mean_3prime_softclipped_bases +HG00240 read1 49290193 49272959 0.99965 45932523 4543946625 4266911175 0.00 0.004599 0.004363 0.000106 100.00 0.00 100.00 0.00 100 100 98.82 49091197 0.99631 1213329 0.02462 0 0.50414 0.01790 0.01184 0.00000 21.59 +HG00240 read2 49290193 49096151 0.99606 45744255 4501617843 4174244580 0.00 0.006610 0.006364 0.000109 100.00 0.00 100.00 0.00 100 100 98.25 49091194 0.99990 1213326 0.02471 0 0.49571 0.01796 0.01744 0.00000 21.78 +HG00240 pair 98580386 98369110 0.99786 91676778 9045564468 8441155755 0.00 0.005600 0.005359 0.000107 100.00 0.00 100.00 0.00 100 100 98.53 98182391 0.99810 2426655 0.02467 0 0.49993 0.01793 0.01464 0.00000 21.70 diff --git a/data/modules/riker/alignment/HG03953.alignment-metrics.txt b/data/modules/riker/alignment/HG03953.alignment-metrics.txt new file mode 100644 index 00000000..fd051e9c --- /dev/null +++ b/data/modules/riker/alignment/HG03953.alignment-metrics.txt @@ -0,0 +1,4 @@ +sample category total_reads aligned_reads frac_aligned hq_aligned_reads hq_aligned_bases hq_aligned_q20_bases hq_median_mismatches mismatch_rate hq_mismatch_rate indel_rate mean_read_length sd_read_length median_read_length mad_read_length min_read_length max_read_length mean_aligned_read_length aligned_reads_in_pairs frac_aligned_in_pairs reads_improperly_paired frac_reads_improperly_paired bad_cycles strand_balance frac_chimeras frac_softclipped_reads frac_hardclipped_reads mean_3prime_softclipped_bases +HG03953 read1 25439946 25432219 0.99970 23891276 3564333695 3501056033 0.00 0.004673 0.003977 0.000235 150.00 0.00 150.00 0.00 150 150 148.70 25366838 0.99743 632030 0.02485 0 0.50057 0.00694 0.00867 0.00000 39.34 +HG03953 read2 25439946 25370547 0.99727 23659859 3522438310 3456502740 0.00 0.004889 0.004102 0.000243 150.00 0.00 150.00 0.00 150 150 147.83 25366838 0.99985 632030 0.02491 0 0.50081 0.00735 0.01441 0.00000 44.38 +HG03953 pair 50879892 50802766 0.99848 47551135 7086772005 6957558773 0.00 0.004780 0.004039 0.000239 150.00 0.00 150.00 0.00 150 150 148.27 50733676 0.99864 1264060 0.02488 0 0.50069 0.00714 0.01154 0.00000 42.26 diff --git a/data/modules/riker/basic/HG00240.base-distribution-by-cycle.txt b/data/modules/riker/basic/HG00240.base-distribution-by-cycle.txt new file mode 100644 index 00000000..dd2c9e82 --- /dev/null +++ b/data/modules/riker/basic/HG00240.base-distribution-by-cycle.txt @@ -0,0 +1,201 @@ +sample read_end cycle frac_a frac_c frac_g frac_t frac_n +HG00240 1 1 0.28942 0.20943 0.20676 0.29184 0.00255 +HG00240 1 2 0.28603 0.21469 0.21071 0.28856 0.00001 +HG00240 1 3 0.27908 0.22161 0.21724 0.28207 0.00001 +HG00240 1 4 0.27963 0.22114 0.21697 0.28226 0.00000 +HG00240 1 5 0.28747 0.21336 0.20914 0.29003 0.00000 +HG00240 1 6 0.28123 0.21971 0.21554 0.28352 0.00000 +HG00240 1 7 0.27907 0.22193 0.21783 0.28117 0.00000 +HG00240 1 8 0.28494 0.21586 0.21183 0.28738 0.00000 +HG00240 1 9 0.28308 0.21768 0.21359 0.28565 0.00000 +HG00240 1 10 0.28043 0.22036 0.21610 0.28312 0.00000 +HG00240 1 11 0.28172 0.21908 0.21480 0.28440 0.00000 +HG00240 1 12 0.28060 0.22020 0.21583 0.28336 0.00000 +HG00240 1 13 0.28170 0.21913 0.21463 0.28453 0.00000 +HG00240 1 14 0.28088 0.22014 0.21549 0.28348 0.00000 +HG00240 1 15 0.27973 0.22129 0.21651 0.28226 0.00021 +HG00240 1 16 0.27960 0.22154 0.21682 0.28203 0.00001 +HG00240 1 17 0.27780 0.22155 0.21685 0.28052 0.00328 +HG00240 1 18 0.27773 0.22327 0.21844 0.28056 0.00000 +HG00240 1 19 0.27768 0.22341 0.21849 0.28042 0.00000 +HG00240 1 20 0.27778 0.22352 0.21834 0.28036 0.00000 +HG00240 1 21 0.27704 0.22424 0.21899 0.27973 0.00000 +HG00240 1 22 0.27685 0.22416 0.21898 0.28001 0.00000 +HG00240 1 23 0.27700 0.22403 0.21880 0.28017 0.00000 +HG00240 1 24 0.27594 0.22520 0.21981 0.27903 0.00001 +HG00240 1 25 0.27612 0.22492 0.21959 0.27935 0.00001 +HG00240 1 26 0.27612 0.22497 0.21947 0.27936 0.00008 +HG00240 1 27 0.27527 0.22576 0.22039 0.27849 0.00009 +HG00240 1 28 0.27515 0.22579 0.22026 0.27869 0.00011 +HG00240 1 29 0.27519 0.22591 0.22026 0.27850 0.00014 +HG00240 1 30 0.27446 0.22665 0.22082 0.27800 0.00007 +HG00240 1 31 0.27430 0.22663 0.22118 0.27784 0.00006 +HG00240 1 32 0.27434 0.22671 0.22095 0.27795 0.00005 +HG00240 1 33 0.27360 0.22746 0.22159 0.27728 0.00006 +HG00240 1 34 0.27363 0.22734 0.22143 0.27752 0.00008 +HG00240 1 35 0.27343 0.22743 0.22155 0.27750 0.00009 +HG00240 1 36 0.27300 0.22789 0.22209 0.27694 0.00008 +HG00240 1 37 0.27321 0.22780 0.22169 0.27728 0.00001 +HG00240 1 38 0.27313 0.22790 0.22165 0.27727 0.00005 +HG00240 1 39 0.27249 0.22835 0.22219 0.27692 0.00006 +HG00240 1 40 0.27269 0.22828 0.22200 0.27698 0.00005 +HG00240 1 41 0.27255 0.22836 0.22197 0.27704 0.00008 +HG00240 1 42 0.27195 0.22894 0.22254 0.27649 0.00008 +HG00240 1 43 0.27224 0.22878 0.22232 0.27658 0.00008 +HG00240 1 44 0.27224 0.22871 0.22221 0.27676 0.00008 +HG00240 1 45 0.27153 0.22927 0.22286 0.27615 0.00018 +HG00240 1 46 0.27159 0.22935 0.22266 0.27616 0.00023 +HG00240 1 47 0.27140 0.22951 0.22286 0.27602 0.00022 +HG00240 1 48 0.27113 0.22985 0.22306 0.27577 0.00020 +HG00240 1 49 0.27090 0.23001 0.22318 0.27563 0.00027 +HG00240 1 50 0.27129 0.22951 0.22302 0.27595 0.00023 +HG00240 1 51 0.27059 0.23025 0.22339 0.27553 0.00024 +HG00240 1 52 0.27062 0.23028 0.22341 0.27553 0.00016 +HG00240 1 53 0.27079 0.23013 0.22317 0.27580 0.00011 +HG00240 1 54 0.27021 0.23078 0.22359 0.27529 0.00013 +HG00240 1 55 0.27042 0.23051 0.22349 0.27544 0.00014 +HG00240 1 56 0.27035 0.23049 0.22350 0.27552 0.00014 +HG00240 1 57 0.26989 0.23103 0.22388 0.27505 0.00016 +HG00240 1 58 0.26989 0.23105 0.22378 0.27517 0.00012 +HG00240 1 59 0.26997 0.23101 0.22367 0.27518 0.00016 +HG00240 1 60 0.26924 0.23160 0.22442 0.27458 0.00017 +HG00240 1 61 0.26943 0.23137 0.22426 0.27475 0.00019 +HG00240 1 62 0.26956 0.23142 0.22404 0.27480 0.00018 +HG00240 1 63 0.26893 0.23201 0.22466 0.27418 0.00022 +HG00240 1 64 0.26923 0.23176 0.22439 0.27436 0.00027 +HG00240 1 65 0.26894 0.23188 0.22439 0.27439 0.00040 +HG00240 1 66 0.26851 0.23226 0.22487 0.27388 0.00048 +HG00240 1 67 0.26849 0.23240 0.22497 0.27362 0.00053 +HG00240 1 68 0.26851 0.23237 0.22484 0.27368 0.00059 +HG00240 1 69 0.26810 0.23258 0.22520 0.27350 0.00062 +HG00240 1 70 0.26796 0.23280 0.22521 0.27340 0.00063 +HG00240 1 71 0.26796 0.23278 0.22530 0.27347 0.00049 +HG00240 1 72 0.26728 0.23359 0.22578 0.27288 0.00047 +HG00240 1 73 0.26775 0.23324 0.22542 0.27315 0.00044 +HG00240 1 74 0.26765 0.23342 0.22559 0.27302 0.00033 +HG00240 1 75 0.26703 0.23409 0.22603 0.27265 0.00020 +HG00240 1 76 0.26694 0.23398 0.22609 0.27277 0.00023 +HG00240 1 77 0.26713 0.23377 0.22614 0.27265 0.00031 +HG00240 1 78 0.26657 0.23443 0.22653 0.27214 0.00033 +HG00240 1 79 0.26648 0.23464 0.22639 0.27217 0.00033 +HG00240 1 80 0.26656 0.23459 0.22645 0.27211 0.00029 +HG00240 1 81 0.26591 0.23520 0.22711 0.27155 0.00023 +HG00240 1 82 0.26595 0.23509 0.22696 0.27171 0.00029 +HG00240 1 83 0.26603 0.23511 0.22693 0.27164 0.00028 +HG00240 1 84 0.26522 0.23597 0.22765 0.27091 0.00026 +HG00240 1 85 0.26519 0.23592 0.22772 0.27080 0.00037 +HG00240 1 86 0.26503 0.23591 0.22778 0.27081 0.00046 +HG00240 1 87 0.26450 0.23637 0.22820 0.27032 0.00062 +HG00240 1 88 0.26444 0.23651 0.22828 0.27013 0.00064 +HG00240 1 89 0.26451 0.23664 0.22827 0.26999 0.00059 +HG00240 1 90 0.26376 0.23727 0.22884 0.26952 0.00061 +HG00240 1 91 0.26371 0.23746 0.22888 0.26933 0.00062 +HG00240 1 92 0.26357 0.23746 0.22906 0.26918 0.00073 +HG00240 1 93 0.26304 0.23823 0.22933 0.26876 0.00065 +HG00240 1 94 0.26282 0.23847 0.22964 0.26851 0.00055 +HG00240 1 95 0.26263 0.23864 0.22988 0.26842 0.00044 +HG00240 1 96 0.26214 0.23901 0.23034 0.26804 0.00048 +HG00240 1 97 0.26194 0.23940 0.23050 0.26768 0.00047 +HG00240 1 98 0.26187 0.23951 0.23060 0.26759 0.00044 +HG00240 1 99 0.26122 0.24031 0.23128 0.26679 0.00040 +HG00240 1 100 0.26112 0.24022 0.23129 0.26689 0.00048 +HG00240 2 1 0.29624 0.20134 0.20137 0.30061 0.00045 +HG00240 2 2 0.28477 0.21539 0.20992 0.28789 0.00203 +HG00240 2 3 0.27668 0.22268 0.21837 0.28011 0.00216 +HG00240 2 4 0.27777 0.22108 0.21791 0.28102 0.00223 +HG00240 2 5 0.28629 0.21283 0.20942 0.28907 0.00239 +HG00240 2 6 0.27911 0.22011 0.21669 0.28149 0.00260 +HG00240 2 7 0.27806 0.22208 0.21838 0.27996 0.00151 +HG00240 2 8 0.28494 0.21531 0.21188 0.28685 0.00102 +HG00240 2 9 0.28282 0.21746 0.21400 0.28476 0.00097 +HG00240 2 10 0.28078 0.21992 0.21607 0.28289 0.00034 +HG00240 2 11 0.28190 0.21901 0.21487 0.28394 0.00027 +HG00240 2 12 0.28098 0.22009 0.21584 0.28288 0.00021 +HG00240 2 13 0.28210 0.21869 0.21441 0.28461 0.00020 +HG00240 2 14 0.28095 0.22001 0.21545 0.28336 0.00022 +HG00240 2 15 0.28001 0.22101 0.21650 0.28228 0.00020 +HG00240 2 16 0.27977 0.22124 0.21675 0.28202 0.00021 +HG00240 2 17 0.27902 0.22197 0.21739 0.28144 0.00018 +HG00240 2 18 0.27789 0.22310 0.21852 0.28034 0.00015 +HG00240 2 19 0.27795 0.22308 0.21833 0.28038 0.00026 +HG00240 2 20 0.27764 0.22340 0.21836 0.27991 0.00069 +HG00240 2 21 0.27669 0.22388 0.21886 0.27951 0.00105 +HG00240 2 22 0.27668 0.22374 0.21872 0.27941 0.00145 +HG00240 2 23 0.27642 0.22373 0.21864 0.27945 0.00176 +HG00240 2 24 0.27534 0.22506 0.21979 0.27836 0.00145 +HG00240 2 25 0.27570 0.22445 0.21940 0.27905 0.00139 +HG00240 2 26 0.27527 0.22501 0.21972 0.27857 0.00143 +HG00240 2 27 0.27465 0.22590 0.22049 0.27809 0.00087 +HG00240 2 28 0.27469 0.22542 0.22030 0.27788 0.00170 +HG00240 2 29 0.27461 0.22569 0.22011 0.27801 0.00159 +HG00240 2 30 0.27365 0.22649 0.22111 0.27727 0.00148 +HG00240 2 31 0.27375 0.22663 0.22117 0.27712 0.00132 +HG00240 2 32 0.27352 0.22696 0.22126 0.27701 0.00125 +HG00240 2 33 0.27318 0.22786 0.22199 0.27674 0.00023 +HG00240 2 34 0.27327 0.22753 0.22150 0.27716 0.00053 +HG00240 2 35 0.27208 0.22699 0.22112 0.27603 0.00378 +HG00240 2 36 0.27252 0.22843 0.22252 0.27643 0.00011 +HG00240 2 37 0.27303 0.22797 0.22191 0.27697 0.00011 +HG00240 2 38 0.27273 0.22828 0.22201 0.27679 0.00019 +HG00240 2 39 0.27224 0.22877 0.22264 0.27620 0.00015 +HG00240 2 40 0.27240 0.22848 0.22222 0.27672 0.00018 +HG00240 2 41 0.27220 0.22867 0.22223 0.27659 0.00031 +HG00240 2 42 0.27157 0.22921 0.22308 0.27581 0.00033 +HG00240 2 43 0.27154 0.22878 0.22250 0.27600 0.00118 +HG00240 2 44 0.27138 0.22892 0.22239 0.27584 0.00147 +HG00240 2 45 0.27069 0.22959 0.22295 0.27516 0.00161 +HG00240 2 46 0.27085 0.22933 0.22305 0.27551 0.00125 +HG00240 2 47 0.27051 0.22939 0.22254 0.27517 0.00239 +HG00240 2 48 0.26998 0.22992 0.22333 0.27470 0.00207 +HG00240 2 49 0.27018 0.22987 0.22320 0.27503 0.00171 +HG00240 2 50 0.27039 0.22975 0.22304 0.27486 0.00196 +HG00240 2 51 0.26998 0.23058 0.22389 0.27485 0.00070 +HG00240 2 52 0.26990 0.23050 0.22373 0.27466 0.00120 +HG00240 2 53 0.26993 0.23016 0.22349 0.27478 0.00163 +HG00240 2 54 0.26961 0.23124 0.22415 0.27448 0.00051 +HG00240 2 55 0.26987 0.23083 0.22390 0.27475 0.00065 +HG00240 2 56 0.26966 0.23125 0.22419 0.27463 0.00028 +HG00240 2 57 0.26926 0.23155 0.22455 0.27445 0.00020 +HG00240 2 58 0.26926 0.23127 0.22440 0.27435 0.00072 +HG00240 2 59 0.26926 0.23169 0.22451 0.27432 0.00021 +HG00240 2 60 0.26863 0.23231 0.22512 0.27377 0.00016 +HG00240 2 61 0.26881 0.23197 0.22482 0.27388 0.00051 +HG00240 2 62 0.26860 0.23228 0.22484 0.27384 0.00043 +HG00240 2 63 0.26770 0.23254 0.22529 0.27303 0.00144 +HG00240 2 64 0.26825 0.23211 0.22488 0.27340 0.00135 +HG00240 2 65 0.26820 0.23290 0.22529 0.27323 0.00039 +HG00240 2 66 0.26767 0.23317 0.22572 0.27309 0.00035 +HG00240 2 67 0.26773 0.23317 0.22587 0.27286 0.00037 +HG00240 2 68 0.26734 0.23312 0.22578 0.27265 0.00111 +HG00240 2 69 0.26683 0.23371 0.22602 0.27229 0.00115 +HG00240 2 70 0.26687 0.23359 0.22617 0.27226 0.00112 +HG00240 2 71 0.26670 0.23368 0.22620 0.27203 0.00139 +HG00240 2 72 0.26607 0.23456 0.22687 0.27140 0.00110 +HG00240 2 73 0.26647 0.23401 0.22653 0.27195 0.00105 +HG00240 2 74 0.26628 0.23440 0.22680 0.27154 0.00098 +HG00240 2 75 0.26556 0.23504 0.22733 0.27101 0.00106 +HG00240 2 76 0.26569 0.23497 0.22707 0.27122 0.00105 +HG00240 2 77 0.26556 0.23496 0.22723 0.27104 0.00120 +HG00240 2 78 0.26503 0.23559 0.22785 0.27049 0.00104 +HG00240 2 79 0.26504 0.23570 0.22783 0.27055 0.00088 +HG00240 2 80 0.26475 0.23596 0.22799 0.27027 0.00104 +HG00240 2 81 0.26431 0.23641 0.22855 0.26984 0.00088 +HG00240 2 82 0.26424 0.23633 0.22843 0.26981 0.00119 +HG00240 2 83 0.26390 0.23681 0.22874 0.26955 0.00099 +HG00240 2 84 0.26324 0.23762 0.22949 0.26885 0.00080 +HG00240 2 85 0.26360 0.23744 0.22945 0.26900 0.00051 +HG00240 2 86 0.26339 0.23764 0.22949 0.26874 0.00075 +HG00240 2 87 0.26259 0.23839 0.23013 0.26817 0.00073 +HG00240 2 88 0.26249 0.23835 0.23000 0.26801 0.00115 +HG00240 2 89 0.26204 0.23867 0.23033 0.26767 0.00129 +HG00240 2 90 0.26146 0.23931 0.23082 0.26716 0.00124 +HG00240 2 91 0.26140 0.23939 0.23094 0.26703 0.00124 +HG00240 2 92 0.26111 0.23966 0.23121 0.26677 0.00125 +HG00240 2 93 0.25925 0.23950 0.23084 0.26495 0.00546 +HG00240 2 94 0.26021 0.24073 0.23208 0.26574 0.00124 +HG00240 2 95 0.25990 0.24098 0.23238 0.26561 0.00113 +HG00240 2 96 0.25929 0.24177 0.23303 0.26492 0.00099 +HG00240 2 97 0.25930 0.24167 0.23303 0.26482 0.00117 +HG00240 2 98 0.25893 0.24226 0.23325 0.26449 0.00107 +HG00240 2 99 0.25802 0.24299 0.23399 0.26373 0.00126 +HG00240 2 100 0.25826 0.24286 0.23392 0.26385 0.00111 diff --git a/data/modules/riker/basic/HG00240.mean-quality-by-cycle.txt b/data/modules/riker/basic/HG00240.mean-quality-by-cycle.txt new file mode 100644 index 00000000..5599b8a7 --- /dev/null +++ b/data/modules/riker/basic/HG00240.mean-quality-by-cycle.txt @@ -0,0 +1,201 @@ +sample cycle mean_quality +HG00240 1 26.50 +HG00240 2 26.34 +HG00240 3 26.31 +HG00240 4 26.55 +HG00240 5 32.07 +HG00240 6 32.93 +HG00240 7 34.28 +HG00240 8 34.28 +HG00240 9 34.26 +HG00240 10 34.25 +HG00240 11 35.04 +HG00240 12 34.85 +HG00240 13 34.91 +HG00240 14 34.79 +HG00240 15 34.63 +HG00240 16 33.74 +HG00240 17 33.91 +HG00240 18 34.79 +HG00240 19 35.40 +HG00240 20 34.73 +HG00240 21 34.61 +HG00240 22 34.70 +HG00240 23 35.13 +HG00240 24 34.75 +HG00240 25 35.26 +HG00240 26 35.21 +HG00240 27 34.53 +HG00240 28 34.97 +HG00240 29 33.28 +HG00240 30 34.96 +HG00240 31 34.97 +HG00240 32 34.90 +HG00240 33 34.92 +HG00240 34 34.96 +HG00240 35 34.84 +HG00240 36 34.84 +HG00240 37 34.83 +HG00240 38 34.69 +HG00240 39 34.79 +HG00240 40 34.62 +HG00240 41 34.54 +HG00240 42 34.57 +HG00240 43 34.48 +HG00240 44 34.28 +HG00240 45 34.32 +HG00240 46 34.28 +HG00240 47 33.82 +HG00240 48 34.17 +HG00240 49 33.55 +HG00240 50 34.02 +HG00240 51 33.98 +HG00240 52 34.02 +HG00240 53 33.83 +HG00240 54 34.03 +HG00240 55 33.69 +HG00240 56 33.61 +HG00240 57 33.67 +HG00240 58 33.90 +HG00240 59 33.82 +HG00240 60 33.45 +HG00240 61 33.38 +HG00240 62 33.29 +HG00240 63 33.12 +HG00240 64 32.91 +HG00240 65 33.10 +HG00240 66 33.07 +HG00240 67 32.98 +HG00240 68 32.16 +HG00240 69 32.62 +HG00240 70 32.58 +HG00240 71 32.03 +HG00240 72 32.38 +HG00240 73 32.13 +HG00240 74 32.02 +HG00240 75 31.71 +HG00240 76 31.81 +HG00240 77 31.60 +HG00240 78 31.49 +HG00240 79 31.23 +HG00240 80 31.01 +HG00240 81 31.19 +HG00240 82 30.78 +HG00240 83 30.60 +HG00240 84 30.41 +HG00240 85 30.05 +HG00240 86 30.20 +HG00240 87 29.84 +HG00240 88 29.59 +HG00240 89 29.25 +HG00240 90 29.01 +HG00240 91 29.07 +HG00240 92 28.73 +HG00240 93 28.46 +HG00240 94 28.22 +HG00240 95 27.77 +HG00240 96 27.53 +HG00240 97 25.58 +HG00240 98 24.94 +HG00240 99 25.03 +HG00240 100 25.05 +HG00240 101 26.67 +HG00240 102 26.24 +HG00240 103 26.16 +HG00240 104 26.53 +HG00240 105 31.91 +HG00240 106 32.45 +HG00240 107 32.78 +HG00240 108 33.92 +HG00240 109 34.03 +HG00240 110 34.00 +HG00240 111 34.13 +HG00240 112 34.08 +HG00240 113 33.97 +HG00240 114 33.90 +HG00240 115 33.78 +HG00240 116 34.26 +HG00240 117 34.43 +HG00240 118 34.24 +HG00240 119 35.00 +HG00240 120 34.29 +HG00240 121 34.93 +HG00240 122 34.18 +HG00240 123 34.84 +HG00240 124 34.78 +HG00240 125 34.76 +HG00240 126 34.41 +HG00240 127 34.69 +HG00240 128 34.68 +HG00240 129 34.27 +HG00240 130 34.47 +HG00240 131 34.45 +HG00240 132 33.74 +HG00240 133 34.33 +HG00240 134 34.41 +HG00240 135 33.85 +HG00240 136 34.37 +HG00240 137 34.42 +HG00240 138 34.10 +HG00240 139 34.19 +HG00240 140 34.20 +HG00240 141 33.71 +HG00240 142 34.15 +HG00240 143 34.15 +HG00240 144 34.04 +HG00240 145 33.91 +HG00240 146 33.95 +HG00240 147 33.94 +HG00240 148 33.72 +HG00240 149 33.58 +HG00240 150 33.02 +HG00240 151 33.71 +HG00240 152 33.42 +HG00240 153 33.18 +HG00240 154 33.16 +HG00240 155 33.20 +HG00240 156 33.18 +HG00240 157 33.03 +HG00240 158 33.12 +HG00240 159 32.79 +HG00240 160 31.75 +HG00240 161 32.93 +HG00240 162 32.74 +HG00240 163 32.58 +HG00240 164 32.35 +HG00240 165 32.11 +HG00240 166 32.40 +HG00240 167 32.08 +HG00240 168 31.99 +HG00240 169 31.86 +HG00240 170 31.65 +HG00240 171 31.58 +HG00240 172 31.27 +HG00240 173 31.11 +HG00240 174 30.04 +HG00240 175 30.64 +HG00240 176 29.88 +HG00240 177 30.46 +HG00240 178 30.12 +HG00240 179 29.94 +HG00240 180 29.58 +HG00240 181 29.89 +HG00240 182 29.44 +HG00240 183 26.81 +HG00240 184 28.88 +HG00240 185 28.67 +HG00240 186 28.82 +HG00240 187 28.30 +HG00240 188 27.98 +HG00240 189 27.69 +HG00240 190 27.36 +HG00240 191 27.55 +HG00240 192 26.94 +HG00240 193 25.10 +HG00240 194 26.09 +HG00240 195 25.77 +HG00240 196 25.43 +HG00240 197 23.79 +HG00240 198 23.09 +HG00240 199 23.20 +HG00240 200 22.91 diff --git a/data/modules/riker/basic/HG00240.quality-score-distribution.txt b/data/modules/riker/basic/HG00240.quality-score-distribution.txt new file mode 100644 index 00000000..e52fba45 --- /dev/null +++ b/data/modules/riker/basic/HG00240.quality-score-distribution.txt @@ -0,0 +1,8 @@ +sample quality count frac_bases +HG00240 1 2735244 0.00028 +HG00240 6 696483380 0.07070 +HG00240 15 105248183 0.01068 +HG00240 22 192281327 0.01952 +HG00240 27 859604804 0.08726 +HG00240 33 3232006455 0.32807 +HG00240 37 4763130754 0.48349 diff --git a/data/modules/riker/basic/HG03953.base-distribution-by-cycle.txt b/data/modules/riker/basic/HG03953.base-distribution-by-cycle.txt new file mode 100644 index 00000000..1f58bdf9 --- /dev/null +++ b/data/modules/riker/basic/HG03953.base-distribution-by-cycle.txt @@ -0,0 +1,301 @@ +sample read_end cycle frac_a frac_c frac_g frac_t frac_n +HG03953 1 1 0.30975 0.18919 0.19019 0.31022 0.00065 +HG03953 1 2 0.30713 0.19160 0.19281 0.30819 0.00027 +HG03953 1 3 0.30462 0.19428 0.19553 0.30557 0.00000 +HG03953 1 4 0.30297 0.19619 0.19728 0.30355 0.00001 +HG03953 1 5 0.30289 0.19593 0.19741 0.30377 0.00000 +HG03953 1 6 0.29902 0.19995 0.20136 0.29967 0.00000 +HG03953 1 7 0.30009 0.19900 0.20029 0.30060 0.00001 +HG03953 1 8 0.30112 0.19832 0.19923 0.30132 0.00000 +HG03953 1 9 0.30170 0.19760 0.19878 0.30192 0.00000 +HG03953 1 10 0.29928 0.19991 0.20117 0.29964 0.00000 +HG03953 1 11 0.30018 0.19903 0.19999 0.30081 0.00000 +HG03953 1 12 0.29995 0.19940 0.20026 0.30039 0.00000 +HG03953 1 13 0.30100 0.19803 0.19923 0.30173 0.00000 +HG03953 1 14 0.30030 0.19868 0.19982 0.30121 0.00000 +HG03953 1 15 0.29995 0.19904 0.20032 0.30070 0.00000 +HG03953 1 16 0.30011 0.19908 0.20017 0.30064 0.00000 +HG03953 1 17 0.30006 0.19912 0.20017 0.30065 0.00000 +HG03953 1 18 0.29951 0.19962 0.20060 0.30027 0.00000 +HG03953 1 19 0.29910 0.19990 0.20126 0.29974 0.00000 +HG03953 1 20 0.29843 0.20070 0.20187 0.29900 0.00000 +HG03953 1 21 0.29835 0.20080 0.20199 0.29885 0.00001 +HG03953 1 22 0.29789 0.20143 0.20239 0.29826 0.00003 +HG03953 1 23 0.29802 0.20130 0.20233 0.29835 0.00000 +HG03953 1 24 0.29704 0.20223 0.20346 0.29727 0.00000 +HG03953 1 25 0.29737 0.20181 0.20321 0.29761 0.00000 +HG03953 1 26 0.29704 0.20209 0.20336 0.29751 0.00000 +HG03953 1 27 0.29662 0.20253 0.20367 0.29718 0.00000 +HG03953 1 28 0.29666 0.20270 0.20361 0.29703 0.00000 +HG03953 1 29 0.29646 0.20266 0.20378 0.29710 0.00001 +HG03953 1 30 0.29597 0.20307 0.20445 0.29651 0.00000 +HG03953 1 31 0.29580 0.20328 0.20458 0.29634 0.00001 +HG03953 1 32 0.29555 0.20347 0.20477 0.29621 0.00000 +HG03953 1 33 0.29556 0.20350 0.20491 0.29602 0.00000 +HG03953 1 34 0.29557 0.20364 0.20479 0.29600 0.00000 +HG03953 1 35 0.29473 0.20415 0.20550 0.29560 0.00003 +HG03953 1 36 0.29519 0.20392 0.20515 0.29575 0.00000 +HG03953 1 37 0.29540 0.20359 0.20496 0.29604 0.00000 +HG03953 1 38 0.29508 0.20400 0.20541 0.29551 0.00000 +HG03953 1 39 0.29490 0.20431 0.20549 0.29530 0.00000 +HG03953 1 40 0.29471 0.20434 0.20585 0.29509 0.00000 +HG03953 1 41 0.29471 0.20432 0.20558 0.29539 0.00000 +HG03953 1 42 0.29445 0.20436 0.20579 0.29540 0.00000 +HG03953 1 43 0.29448 0.20436 0.20567 0.29548 0.00000 +HG03953 1 44 0.29409 0.20486 0.20609 0.29496 0.00001 +HG03953 1 45 0.29411 0.20500 0.20608 0.29481 0.00000 +HG03953 1 46 0.29438 0.20471 0.20603 0.29487 0.00001 +HG03953 1 47 0.29431 0.20475 0.20603 0.29490 0.00001 +HG03953 1 48 0.29428 0.20499 0.20618 0.29455 0.00000 +HG03953 1 49 0.29391 0.20514 0.20630 0.29465 0.00001 +HG03953 1 50 0.29386 0.20507 0.20627 0.29480 0.00001 +HG03953 1 51 0.29414 0.20482 0.20610 0.29494 0.00000 +HG03953 1 52 0.29386 0.20510 0.20617 0.29486 0.00000 +HG03953 1 53 0.29412 0.20487 0.20599 0.29501 0.00000 +HG03953 1 54 0.29393 0.20506 0.20633 0.29467 0.00001 +HG03953 1 55 0.29362 0.20548 0.20662 0.29428 0.00000 +HG03953 1 56 0.29343 0.20548 0.20659 0.29447 0.00003 +HG03953 1 57 0.29377 0.20522 0.20625 0.29476 0.00000 +HG03953 1 58 0.29391 0.20518 0.20599 0.29491 0.00000 +HG03953 1 59 0.29333 0.20549 0.20653 0.29464 0.00001 +HG03953 1 60 0.29341 0.20567 0.20686 0.29404 0.00002 +HG03953 1 61 0.29343 0.20566 0.20674 0.29416 0.00001 +HG03953 1 62 0.29356 0.20548 0.20645 0.29450 0.00000 +HG03953 1 63 0.29396 0.20510 0.20656 0.29437 0.00000 +HG03953 1 64 0.29359 0.20534 0.20689 0.29418 0.00000 +HG03953 1 65 0.29347 0.20560 0.20674 0.29419 0.00000 +HG03953 1 66 0.29353 0.20559 0.20658 0.29429 0.00000 +HG03953 1 67 0.29343 0.20559 0.20682 0.29415 0.00001 +HG03953 1 68 0.29378 0.20534 0.20651 0.29437 0.00000 +HG03953 1 69 0.29333 0.20552 0.20697 0.29418 0.00000 +HG03953 1 70 0.29317 0.20575 0.20719 0.29388 0.00000 +HG03953 1 71 0.29316 0.20585 0.20720 0.29379 0.00000 +HG03953 1 72 0.29318 0.20588 0.20693 0.29400 0.00000 +HG03953 1 73 0.29337 0.20573 0.20691 0.29399 0.00000 +HG03953 1 74 0.29345 0.20566 0.20699 0.29389 0.00001 +HG03953 1 75 0.29312 0.20590 0.20713 0.29385 0.00000 +HG03953 1 76 0.29315 0.20588 0.20713 0.29384 0.00000 +HG03953 1 77 0.29326 0.20545 0.20696 0.29433 0.00000 +HG03953 1 78 0.29333 0.20570 0.20694 0.29402 0.00000 +HG03953 1 79 0.29309 0.20594 0.20729 0.29368 0.00001 +HG03953 1 80 0.29279 0.20622 0.20751 0.29346 0.00002 +HG03953 1 81 0.29321 0.20570 0.20714 0.29394 0.00000 +HG03953 1 82 0.29349 0.20581 0.20673 0.29397 0.00000 +HG03953 1 83 0.29364 0.20540 0.20649 0.29446 0.00000 +HG03953 1 84 0.29305 0.20602 0.20727 0.29365 0.00002 +HG03953 1 85 0.29312 0.20595 0.20723 0.29370 0.00000 +HG03953 1 86 0.29354 0.20562 0.20672 0.29411 0.00000 +HG03953 1 87 0.29329 0.20560 0.20693 0.29417 0.00000 +HG03953 1 88 0.29324 0.20588 0.20716 0.29371 0.00001 +HG03953 1 89 0.29320 0.20615 0.20709 0.29355 0.00001 +HG03953 1 90 0.29299 0.20609 0.20730 0.29362 0.00001 +HG03953 1 91 0.29299 0.20593 0.20749 0.29359 0.00000 +HG03953 1 92 0.29323 0.20581 0.20711 0.29385 0.00000 +HG03953 1 93 0.29335 0.20574 0.20707 0.29384 0.00000 +HG03953 1 94 0.29301 0.20615 0.20740 0.29343 0.00001 +HG03953 1 95 0.29299 0.20596 0.20746 0.29357 0.00002 +HG03953 1 96 0.29272 0.20626 0.20750 0.29352 0.00001 +HG03953 1 97 0.29288 0.20610 0.20715 0.29386 0.00000 +HG03953 1 98 0.29323 0.20587 0.20714 0.29374 0.00001 +HG03953 1 99 0.29291 0.20603 0.20744 0.29362 0.00001 +HG03953 1 100 0.29280 0.20615 0.20771 0.29334 0.00000 +HG03953 1 101 0.29267 0.20620 0.20771 0.29341 0.00000 +HG03953 1 102 0.29302 0.20603 0.20728 0.29367 0.00001 +HG03953 1 103 0.29306 0.20611 0.20739 0.29344 0.00000 +HG03953 1 104 0.29280 0.20610 0.20775 0.29335 0.00000 +HG03953 1 105 0.29278 0.20616 0.20771 0.29333 0.00001 +HG03953 1 106 0.29292 0.20609 0.20721 0.29377 0.00001 +HG03953 1 107 0.29311 0.20578 0.20718 0.29387 0.00005 +HG03953 1 108 0.29318 0.20584 0.20716 0.29381 0.00000 +HG03953 1 109 0.29289 0.20610 0.20736 0.29364 0.00001 +HG03953 1 110 0.29287 0.20606 0.20729 0.29377 0.00002 +HG03953 1 111 0.29299 0.20582 0.20745 0.29373 0.00000 +HG03953 1 112 0.29285 0.20602 0.20727 0.29387 0.00000 +HG03953 1 113 0.29310 0.20580 0.20713 0.29395 0.00002 +HG03953 1 114 0.29309 0.20582 0.20710 0.29398 0.00001 +HG03953 1 115 0.29281 0.20603 0.20753 0.29362 0.00002 +HG03953 1 116 0.29291 0.20603 0.20743 0.29363 0.00000 +HG03953 1 117 0.29285 0.20585 0.20761 0.29369 0.00000 +HG03953 1 118 0.29305 0.20608 0.20719 0.29365 0.00003 +HG03953 1 119 0.29304 0.20589 0.20745 0.29361 0.00001 +HG03953 1 120 0.29263 0.20614 0.20773 0.29348 0.00002 +HG03953 1 121 0.29259 0.20621 0.20754 0.29365 0.00002 +HG03953 1 122 0.29302 0.20589 0.20728 0.29378 0.00003 +HG03953 1 123 0.29321 0.20584 0.20736 0.29359 0.00000 +HG03953 1 124 0.29286 0.20604 0.20744 0.29362 0.00004 +HG03953 1 125 0.29281 0.20597 0.20756 0.29362 0.00003 +HG03953 1 126 0.29295 0.20590 0.20743 0.29368 0.00004 +HG03953 1 127 0.29305 0.20585 0.20726 0.29383 0.00000 +HG03953 1 128 0.29317 0.20587 0.20732 0.29360 0.00004 +HG03953 1 129 0.29280 0.20598 0.20752 0.29366 0.00004 +HG03953 1 130 0.29280 0.20609 0.20753 0.29359 0.00000 +HG03953 1 131 0.29293 0.20607 0.20737 0.29359 0.00004 +HG03953 1 132 0.29305 0.20609 0.20731 0.29353 0.00003 +HG03953 1 133 0.29295 0.20604 0.20728 0.29371 0.00001 +HG03953 1 134 0.29266 0.20616 0.20760 0.29356 0.00002 +HG03953 1 135 0.29280 0.20616 0.20761 0.29339 0.00004 +HG03953 1 136 0.29283 0.20601 0.20743 0.29372 0.00001 +HG03953 1 137 0.29333 0.20571 0.20726 0.29370 0.00000 +HG03953 1 138 0.29322 0.20569 0.20724 0.29383 0.00002 +HG03953 1 139 0.29295 0.20583 0.20739 0.29360 0.00024 +HG03953 1 140 0.29313 0.20580 0.20749 0.29353 0.00005 +HG03953 1 141 0.29325 0.20573 0.20731 0.29367 0.00004 +HG03953 1 142 0.29336 0.20572 0.20711 0.29377 0.00005 +HG03953 1 143 0.29337 0.20570 0.20706 0.29382 0.00004 +HG03953 1 144 0.29311 0.20590 0.20727 0.29369 0.00003 +HG03953 1 145 0.29308 0.20584 0.20736 0.29369 0.00003 +HG03953 1 146 0.29320 0.20556 0.20722 0.29396 0.00006 +HG03953 1 147 0.29359 0.20546 0.20683 0.29408 0.00003 +HG03953 1 148 0.29369 0.20534 0.20673 0.29421 0.00002 +HG03953 1 149 0.29353 0.20549 0.20684 0.29411 0.00003 +HG03953 1 150 0.29344 0.20553 0.20689 0.29414 0.00001 +HG03953 2 1 0.31019 0.18710 0.19115 0.31076 0.00079 +HG03953 2 2 0.30655 0.19108 0.19517 0.30715 0.00004 +HG03953 2 3 0.30220 0.19552 0.19956 0.30271 0.00002 +HG03953 2 4 0.29930 0.19848 0.20248 0.29972 0.00001 +HG03953 2 5 0.30228 0.19528 0.19961 0.30283 0.00000 +HG03953 2 6 0.29601 0.20150 0.20571 0.29677 0.00001 +HG03953 2 7 0.29802 0.19991 0.20400 0.29805 0.00002 +HG03953 2 8 0.29995 0.19790 0.20195 0.30017 0.00003 +HG03953 2 9 0.30027 0.19742 0.20160 0.30071 0.00000 +HG03953 2 10 0.29799 0.19976 0.20380 0.29845 0.00000 +HG03953 2 11 0.29941 0.19822 0.20247 0.29989 0.00001 +HG03953 2 12 0.29920 0.19819 0.20252 0.30008 0.00001 +HG03953 2 13 0.30096 0.19657 0.20072 0.30172 0.00002 +HG03953 2 14 0.29995 0.19725 0.20173 0.30106 0.00000 +HG03953 2 15 0.29932 0.19771 0.20230 0.30067 0.00000 +HG03953 2 16 0.29927 0.19798 0.20248 0.30026 0.00001 +HG03953 2 17 0.29916 0.19809 0.20251 0.30018 0.00007 +HG03953 2 18 0.29873 0.19844 0.20284 0.29985 0.00014 +HG03953 2 19 0.29832 0.19870 0.20332 0.29954 0.00013 +HG03953 2 20 0.29760 0.19941 0.20403 0.29888 0.00008 +HG03953 2 21 0.29786 0.19932 0.20373 0.29903 0.00007 +HG03953 2 22 0.29732 0.19977 0.20439 0.29846 0.00007 +HG03953 2 23 0.29747 0.19971 0.20437 0.29838 0.00007 +HG03953 2 24 0.29632 0.20052 0.20546 0.29762 0.00008 +HG03953 2 25 0.29660 0.20040 0.20511 0.29781 0.00008 +HG03953 2 26 0.29630 0.20069 0.20558 0.29736 0.00007 +HG03953 2 27 0.29563 0.20138 0.20593 0.29692 0.00013 +HG03953 2 28 0.29586 0.20127 0.20579 0.29694 0.00014 +HG03953 2 29 0.29552 0.20130 0.20606 0.29699 0.00014 +HG03953 2 30 0.29522 0.20161 0.20635 0.29666 0.00016 +HG03953 2 31 0.29493 0.20196 0.20650 0.29648 0.00014 +HG03953 2 32 0.29476 0.20213 0.20671 0.29625 0.00014 +HG03953 2 33 0.29470 0.20217 0.20679 0.29622 0.00013 +HG03953 2 34 0.29482 0.20220 0.20673 0.29604 0.00020 +HG03953 2 35 0.29412 0.20273 0.20734 0.29554 0.00027 +HG03953 2 36 0.29435 0.20264 0.20718 0.29556 0.00028 +HG03953 2 37 0.29458 0.20238 0.20667 0.29610 0.00027 +HG03953 2 38 0.29419 0.20276 0.20722 0.29555 0.00028 +HG03953 2 39 0.29419 0.20272 0.20732 0.29544 0.00034 +HG03953 2 40 0.29379 0.20302 0.20743 0.29549 0.00028 +HG03953 2 41 0.29373 0.20289 0.20738 0.29552 0.00048 +HG03953 2 42 0.29377 0.20286 0.20747 0.29548 0.00042 +HG03953 2 43 0.29380 0.20286 0.20727 0.29558 0.00048 +HG03953 2 44 0.29356 0.20326 0.20758 0.29506 0.00055 +HG03953 2 45 0.29330 0.20336 0.20796 0.29490 0.00048 +HG03953 2 46 0.29353 0.20312 0.20757 0.29530 0.00048 +HG03953 2 47 0.29350 0.20330 0.20776 0.29489 0.00055 +HG03953 2 48 0.29337 0.20355 0.20769 0.29479 0.00061 +HG03953 2 49 0.29332 0.20356 0.20777 0.29473 0.00061 +HG03953 2 50 0.29314 0.20367 0.20801 0.29458 0.00061 +HG03953 2 51 0.29328 0.20331 0.20790 0.29483 0.00068 +HG03953 2 52 0.29321 0.20344 0.20774 0.29486 0.00076 +HG03953 2 53 0.29336 0.20327 0.20745 0.29504 0.00089 +HG03953 2 54 0.29322 0.20336 0.20781 0.29465 0.00095 +HG03953 2 55 0.29269 0.20380 0.20823 0.29427 0.00102 +HG03953 2 56 0.29268 0.20374 0.20826 0.29422 0.00110 +HG03953 2 57 0.29296 0.20357 0.20760 0.29483 0.00103 +HG03953 2 58 0.29307 0.20353 0.20746 0.29486 0.00108 +HG03953 2 59 0.29273 0.20358 0.20813 0.29448 0.00109 +HG03953 2 60 0.29251 0.20412 0.20832 0.29395 0.00110 +HG03953 2 61 0.29262 0.20385 0.20844 0.29400 0.00109 +HG03953 2 62 0.29299 0.20388 0.20792 0.29412 0.00109 +HG03953 2 63 0.29326 0.20346 0.20786 0.29434 0.00109 +HG03953 2 64 0.29283 0.20365 0.20813 0.29423 0.00116 +HG03953 2 65 0.29261 0.20374 0.20838 0.29417 0.00109 +HG03953 2 66 0.29259 0.20392 0.20820 0.29419 0.00110 +HG03953 2 67 0.29279 0.20404 0.20819 0.29390 0.00109 +HG03953 2 68 0.29293 0.20389 0.20770 0.29438 0.00110 +HG03953 2 69 0.29263 0.20392 0.20810 0.29412 0.00123 +HG03953 2 70 0.29208 0.20426 0.20857 0.29393 0.00116 +HG03953 2 71 0.29226 0.20415 0.20845 0.29398 0.00116 +HG03953 2 72 0.29242 0.20432 0.20826 0.29389 0.00110 +HG03953 2 73 0.29291 0.20411 0.20788 0.29400 0.00110 +HG03953 2 74 0.29257 0.20394 0.20808 0.29424 0.00116 +HG03953 2 75 0.29261 0.20424 0.20834 0.29378 0.00104 +HG03953 2 76 0.29252 0.20406 0.20828 0.29388 0.00125 +HG03953 2 77 0.29276 0.20407 0.20783 0.29417 0.00116 +HG03953 2 78 0.29293 0.20395 0.20787 0.29396 0.00129 +HG03953 2 79 0.29261 0.20430 0.20822 0.29363 0.00123 +HG03953 2 80 0.29219 0.20451 0.20849 0.29370 0.00111 +HG03953 2 81 0.29247 0.20399 0.20815 0.29409 0.00129 +HG03953 2 82 0.29279 0.20410 0.20793 0.29408 0.00111 +HG03953 2 83 0.29287 0.20387 0.20758 0.29445 0.00123 +HG03953 2 84 0.29254 0.20434 0.20804 0.29397 0.00110 +HG03953 2 85 0.29224 0.20447 0.20818 0.29386 0.00125 +HG03953 2 86 0.29270 0.20407 0.20820 0.29387 0.00116 +HG03953 2 87 0.29286 0.20397 0.20780 0.29421 0.00116 +HG03953 2 88 0.29261 0.20434 0.20814 0.29369 0.00123 +HG03953 2 89 0.29231 0.20444 0.20830 0.29379 0.00116 +HG03953 2 90 0.29241 0.20457 0.20831 0.29355 0.00116 +HG03953 2 91 0.29243 0.20445 0.20826 0.29360 0.00126 +HG03953 2 92 0.29239 0.20432 0.20830 0.29389 0.00110 +HG03953 2 93 0.29291 0.20417 0.20791 0.29385 0.00117 +HG03953 2 94 0.29228 0.20455 0.20843 0.29361 0.00113 +HG03953 2 95 0.29235 0.20458 0.20846 0.29350 0.00111 +HG03953 2 96 0.29239 0.20448 0.20833 0.29370 0.00111 +HG03953 2 97 0.29230 0.20446 0.20825 0.29386 0.00112 +HG03953 2 98 0.29235 0.20443 0.20810 0.29394 0.00118 +HG03953 2 99 0.29240 0.20454 0.20840 0.29355 0.00110 +HG03953 2 100 0.29211 0.20474 0.20856 0.29342 0.00117 +HG03953 2 101 0.29202 0.20486 0.20887 0.29315 0.00110 +HG03953 2 102 0.29240 0.20443 0.20831 0.29366 0.00121 +HG03953 2 103 0.29263 0.20427 0.20828 0.29357 0.00125 +HG03953 2 104 0.29243 0.20452 0.20854 0.29340 0.00112 +HG03953 2 105 0.29223 0.20455 0.20870 0.29335 0.00117 +HG03953 2 106 0.29254 0.20439 0.20821 0.29376 0.00110 +HG03953 2 107 0.29260 0.20418 0.20804 0.29414 0.00105 +HG03953 2 108 0.29277 0.20421 0.20787 0.29409 0.00106 +HG03953 2 109 0.29245 0.20447 0.20835 0.29362 0.00112 +HG03953 2 110 0.29226 0.20436 0.20824 0.29403 0.00111 +HG03953 2 111 0.29246 0.20434 0.20828 0.29379 0.00112 +HG03953 2 112 0.29227 0.20447 0.20826 0.29383 0.00117 +HG03953 2 113 0.29271 0.20420 0.20784 0.29407 0.00118 +HG03953 2 114 0.29247 0.20427 0.20799 0.29410 0.00117 +HG03953 2 115 0.29232 0.20446 0.20828 0.29376 0.00117 +HG03953 2 116 0.29249 0.20440 0.20815 0.29379 0.00117 +HG03953 2 117 0.29250 0.20447 0.20815 0.29377 0.00112 +HG03953 2 118 0.29265 0.20426 0.20788 0.29409 0.00112 +HG03953 2 119 0.29244 0.20436 0.20818 0.29390 0.00112 +HG03953 2 120 0.29220 0.20470 0.20847 0.29353 0.00111 +HG03953 2 121 0.29224 0.20474 0.20835 0.29351 0.00117 +HG03953 2 122 0.29253 0.20427 0.20807 0.29395 0.00119 +HG03953 2 123 0.29273 0.20423 0.20788 0.29393 0.00123 +HG03953 2 124 0.29250 0.20445 0.20812 0.29376 0.00117 +HG03953 2 125 0.29221 0.20450 0.20834 0.29371 0.00123 +HG03953 2 126 0.29249 0.20421 0.20826 0.29381 0.00124 +HG03953 2 127 0.29252 0.20424 0.20796 0.29404 0.00124 +HG03953 2 128 0.29288 0.20418 0.20787 0.29378 0.00130 +HG03953 2 129 0.29267 0.20429 0.20815 0.29372 0.00118 +HG03953 2 130 0.29249 0.20445 0.20820 0.29369 0.00117 +HG03953 2 131 0.29268 0.20449 0.20826 0.29338 0.00118 +HG03953 2 132 0.29268 0.20450 0.20790 0.29367 0.00125 +HG03953 2 133 0.29245 0.20460 0.20801 0.29374 0.00119 +HG03953 2 134 0.29228 0.20465 0.20841 0.29349 0.00117 +HG03953 2 135 0.29232 0.20467 0.20847 0.29351 0.00104 +HG03953 2 136 0.29280 0.20420 0.20795 0.29389 0.00117 +HG03953 2 137 0.29292 0.20432 0.20777 0.29395 0.00104 +HG03953 2 138 0.29323 0.20409 0.20784 0.29380 0.00104 +HG03953 2 139 0.29262 0.20424 0.20819 0.29384 0.00112 +HG03953 2 140 0.29283 0.20427 0.20813 0.29366 0.00111 +HG03953 2 141 0.29290 0.20434 0.20774 0.29385 0.00117 +HG03953 2 142 0.29323 0.20404 0.20772 0.29385 0.00116 +HG03953 2 143 0.29311 0.20394 0.20772 0.29417 0.00105 +HG03953 2 144 0.29275 0.20419 0.20779 0.29407 0.00119 +HG03953 2 145 0.29271 0.20441 0.20795 0.29376 0.00117 +HG03953 2 146 0.29283 0.20422 0.20776 0.29415 0.00103 +HG03953 2 147 0.29317 0.20390 0.20736 0.29440 0.00116 +HG03953 2 148 0.29341 0.20392 0.20734 0.29423 0.00110 +HG03953 2 149 0.29329 0.20387 0.20739 0.29431 0.00114 +HG03953 2 150 0.29310 0.20400 0.20746 0.29421 0.00123 diff --git a/data/modules/riker/basic/HG03953.mean-quality-by-cycle.txt b/data/modules/riker/basic/HG03953.mean-quality-by-cycle.txt new file mode 100644 index 00000000..4acd804f --- /dev/null +++ b/data/modules/riker/basic/HG03953.mean-quality-by-cycle.txt @@ -0,0 +1,301 @@ +sample cycle mean_quality +HG03953 1 29.59 +HG03953 2 29.63 +HG03953 3 29.65 +HG03953 4 29.69 +HG03953 5 29.77 +HG03953 6 29.75 +HG03953 7 29.78 +HG03953 8 29.80 +HG03953 9 29.80 +HG03953 10 29.81 +HG03953 11 29.81 +HG03953 12 29.82 +HG03953 13 29.82 +HG03953 14 29.81 +HG03953 15 29.82 +HG03953 16 29.82 +HG03953 17 29.82 +HG03953 18 29.82 +HG03953 19 29.81 +HG03953 20 29.79 +HG03953 21 29.80 +HG03953 22 29.81 +HG03953 23 29.80 +HG03953 24 29.79 +HG03953 25 29.77 +HG03953 26 29.72 +HG03953 27 29.71 +HG03953 28 29.69 +HG03953 29 29.71 +HG03953 30 29.68 +HG03953 31 29.67 +HG03953 32 29.68 +HG03953 33 29.67 +HG03953 34 29.65 +HG03953 35 29.65 +HG03953 36 29.66 +HG03953 37 29.63 +HG03953 38 29.64 +HG03953 39 29.62 +HG03953 40 29.63 +HG03953 41 29.64 +HG03953 42 29.62 +HG03953 43 29.59 +HG03953 44 29.58 +HG03953 45 29.59 +HG03953 46 29.61 +HG03953 47 29.59 +HG03953 48 29.58 +HG03953 49 29.59 +HG03953 50 29.56 +HG03953 51 29.56 +HG03953 52 29.55 +HG03953 53 29.54 +HG03953 54 29.54 +HG03953 55 29.56 +HG03953 56 29.54 +HG03953 57 29.53 +HG03953 58 29.53 +HG03953 59 29.53 +HG03953 60 29.52 +HG03953 61 29.52 +HG03953 62 29.50 +HG03953 63 29.51 +HG03953 64 29.50 +HG03953 65 29.48 +HG03953 66 29.48 +HG03953 67 29.49 +HG03953 68 29.49 +HG03953 69 29.48 +HG03953 70 29.48 +HG03953 71 29.48 +HG03953 72 29.48 +HG03953 73 29.45 +HG03953 74 29.45 +HG03953 75 29.44 +HG03953 76 29.44 +HG03953 77 29.44 +HG03953 78 29.44 +HG03953 79 29.44 +HG03953 80 29.42 +HG03953 81 29.42 +HG03953 82 29.41 +HG03953 83 29.42 +HG03953 84 29.40 +HG03953 85 29.38 +HG03953 86 29.37 +HG03953 87 29.36 +HG03953 88 29.36 +HG03953 89 29.36 +HG03953 90 29.38 +HG03953 91 29.36 +HG03953 92 29.34 +HG03953 93 29.35 +HG03953 94 29.34 +HG03953 95 29.34 +HG03953 96 29.32 +HG03953 97 29.31 +HG03953 98 29.32 +HG03953 99 29.30 +HG03953 100 29.31 +HG03953 101 29.31 +HG03953 102 29.29 +HG03953 103 29.29 +HG03953 104 29.30 +HG03953 105 29.28 +HG03953 106 29.27 +HG03953 107 29.26 +HG03953 108 29.26 +HG03953 109 29.27 +HG03953 110 29.24 +HG03953 111 29.24 +HG03953 112 29.25 +HG03953 113 29.24 +HG03953 114 29.19 +HG03953 115 29.19 +HG03953 116 29.21 +HG03953 117 29.22 +HG03953 118 29.20 +HG03953 119 29.21 +HG03953 120 29.18 +HG03953 121 29.18 +HG03953 122 29.17 +HG03953 123 29.17 +HG03953 124 29.16 +HG03953 125 29.17 +HG03953 126 29.17 +HG03953 127 29.15 +HG03953 128 29.14 +HG03953 129 29.14 +HG03953 130 29.12 +HG03953 131 29.10 +HG03953 132 29.07 +HG03953 133 29.04 +HG03953 134 29.10 +HG03953 135 29.11 +HG03953 136 29.09 +HG03953 137 29.05 +HG03953 138 29.05 +HG03953 139 29.05 +HG03953 140 29.04 +HG03953 141 29.06 +HG03953 142 29.08 +HG03953 143 29.07 +HG03953 144 29.03 +HG03953 145 28.97 +HG03953 146 29.03 +HG03953 147 29.03 +HG03953 148 28.99 +HG03953 149 29.15 +HG03953 150 29.14 +HG03953 151 29.81 +HG03953 152 29.79 +HG03953 153 29.76 +HG03953 154 29.76 +HG03953 155 29.78 +HG03953 156 29.73 +HG03953 157 29.74 +HG03953 158 29.70 +HG03953 159 29.73 +HG03953 160 29.72 +HG03953 161 29.71 +HG03953 162 29.70 +HG03953 163 29.70 +HG03953 164 29.68 +HG03953 165 29.68 +HG03953 166 29.67 +HG03953 167 29.67 +HG03953 168 29.66 +HG03953 169 29.66 +HG03953 170 29.66 +HG03953 171 29.66 +HG03953 172 29.64 +HG03953 173 29.64 +HG03953 174 29.63 +HG03953 175 29.62 +HG03953 176 29.62 +HG03953 177 29.59 +HG03953 178 29.58 +HG03953 179 29.60 +HG03953 180 29.59 +HG03953 181 29.56 +HG03953 182 29.58 +HG03953 183 29.57 +HG03953 184 29.55 +HG03953 185 29.52 +HG03953 186 29.52 +HG03953 187 29.52 +HG03953 188 29.51 +HG03953 189 29.50 +HG03953 190 29.50 +HG03953 191 29.49 +HG03953 192 29.50 +HG03953 193 29.49 +HG03953 194 29.48 +HG03953 195 29.46 +HG03953 196 29.46 +HG03953 197 29.46 +HG03953 198 29.44 +HG03953 199 29.44 +HG03953 200 29.44 +HG03953 201 29.43 +HG03953 202 29.43 +HG03953 203 29.43 +HG03953 204 29.42 +HG03953 205 29.39 +HG03953 206 29.39 +HG03953 207 29.38 +HG03953 208 29.38 +HG03953 209 29.37 +HG03953 210 29.35 +HG03953 211 29.37 +HG03953 212 29.36 +HG03953 213 29.36 +HG03953 214 29.34 +HG03953 215 29.34 +HG03953 216 29.33 +HG03953 217 29.33 +HG03953 218 29.33 +HG03953 219 29.32 +HG03953 220 29.29 +HG03953 221 29.30 +HG03953 222 29.30 +HG03953 223 29.29 +HG03953 224 29.29 +HG03953 225 29.27 +HG03953 226 29.25 +HG03953 227 29.28 +HG03953 228 29.26 +HG03953 229 29.25 +HG03953 230 29.24 +HG03953 231 29.27 +HG03953 232 29.25 +HG03953 233 29.25 +HG03953 234 29.24 +HG03953 235 29.21 +HG03953 236 29.21 +HG03953 237 29.18 +HG03953 238 29.20 +HG03953 239 29.18 +HG03953 240 29.18 +HG03953 241 29.18 +HG03953 242 29.17 +HG03953 243 29.17 +HG03953 244 29.17 +HG03953 245 29.17 +HG03953 246 29.18 +HG03953 247 29.15 +HG03953 248 29.13 +HG03953 249 29.11 +HG03953 250 29.11 +HG03953 251 29.09 +HG03953 252 29.11 +HG03953 253 29.11 +HG03953 254 29.09 +HG03953 255 29.07 +HG03953 256 29.05 +HG03953 257 29.09 +HG03953 258 29.05 +HG03953 259 29.02 +HG03953 260 29.02 +HG03953 261 29.03 +HG03953 262 28.99 +HG03953 263 29.01 +HG03953 264 29.00 +HG03953 265 29.02 +HG03953 266 29.00 +HG03953 267 29.03 +HG03953 268 29.02 +HG03953 269 29.00 +HG03953 270 28.97 +HG03953 271 28.96 +HG03953 272 28.95 +HG03953 273 28.95 +HG03953 274 28.95 +HG03953 275 28.98 +HG03953 276 28.94 +HG03953 277 28.95 +HG03953 278 28.91 +HG03953 279 28.87 +HG03953 280 28.86 +HG03953 281 28.90 +HG03953 282 28.87 +HG03953 283 28.86 +HG03953 284 28.89 +HG03953 285 28.80 +HG03953 286 28.86 +HG03953 287 28.84 +HG03953 288 28.86 +HG03953 289 28.81 +HG03953 290 28.79 +HG03953 291 28.81 +HG03953 292 28.82 +HG03953 293 28.79 +HG03953 294 28.84 +HG03953 295 28.81 +HG03953 296 28.88 +HG03953 297 28.76 +HG03953 298 28.68 +HG03953 299 28.92 +HG03953 300 28.90 diff --git a/data/modules/riker/basic/HG03953.quality-score-distribution.txt b/data/modules/riker/basic/HG03953.quality-score-distribution.txt new file mode 100644 index 00000000..c0056362 --- /dev/null +++ b/data/modules/riker/basic/HG03953.quality-score-distribution.txt @@ -0,0 +1,8 @@ +sample quality count frac_bases +HG03953 3 620816 0.00008 +HG03953 4 724879 0.00010 +HG03953 5 2942942 0.00039 +HG03953 6 23332683 0.00306 +HG03953 10 150105887 0.01968 +HG03953 20 117195568 0.01536 +HG03953 30 7333855994 0.96134 diff --git a/data/modules/riker/gcbias/HG03953.gcbias-detail.txt b/data/modules/riker/gcbias/HG03953.gcbias-detail.txt new file mode 100644 index 00000000..bd16e6f5 --- /dev/null +++ b/data/modules/riker/gcbias/HG03953.gcbias-detail.txt @@ -0,0 +1,102 @@ +sample gc windows read_starts reported_base_quality empirical_base_quality normalized_coverage error_bar_width +HG03953 0 139943 1752 28.66 14.42 0.73802 0.01763 +HG03953 1 102415 3123 29.13 18.94 1.79760 0.03217 +HG03953 2 118963 2432 28.85 15.95 1.20514 0.02444 +HG03953 3 152188 17916 25.61 20.16 6.93978 0.05185 +HG03953 4 167741 6689 27.95 15.94 2.35075 0.02874 +HG03953 5 173331 5672 27.15 15.17 1.92906 0.02561 +HG03953 6 196374 8754 27.28 13.54 2.62789 0.02809 +HG03953 7 211224 12377 28.46 13.39 3.45428 0.03105 +HG03953 8 241141 12908 28.39 14.20 3.15554 0.02777 +HG03953 9 270285 17428 27.09 14.19 3.80111 0.02879 +HG03953 10 318092 16492 28.48 13.96 3.05637 0.02380 +HG03953 11 384289 18154 28.36 13.18 2.78484 0.02067 +HG03953 12 493642 20580 27.97 14.04 2.45764 0.01713 +HG03953 13 646401 22830 27.68 14.69 2.08204 0.01378 +HG03953 14 910146 27658 28.21 15.07 1.79141 0.01077 +HG03953 15 1331519 38060 28.15 16.12 1.68503 0.00864 +HG03953 16 1984326 51961 27.85 17.63 1.54365 0.00677 +HG03953 17 2974388 71568 27.98 19.07 1.41843 0.00530 +HG03953 18 4457600 97499 28.57 19.25 1.28939 0.00413 +HG03953 19 6577070 141957 28.84 18.86 1.27236 0.00338 +HG03953 20 9491423 198979 28.93 19.22 1.23584 0.00277 +HG03953 21 13340318 278511 29.04 19.14 1.23073 0.00233 +HG03953 22 18205832 353007 29.11 20.43 1.14303 0.00192 +HG03953 23 24158082 452758 29.17 21.05 1.10481 0.00164 +HG03953 24 31177718 568157 29.21 21.47 1.07426 0.00143 +HG03953 25 39099768 688047 29.24 22.39 1.03736 0.00125 +HG03953 26 47617250 824045 29.28 22.71 1.02017 0.00112 +HG03953 27 56526703 958331 29.30 23.20 0.99942 0.00102 +HG03953 28 65511831 1099052 29.33 23.41 0.98897 0.00094 +HG03953 29 74283104 1236692 29.35 23.51 0.98142 0.00088 +HG03953 30 82645611 1368449 29.36 23.60 0.97610 0.00083 +HG03953 31 90463413 1490378 29.38 23.62 0.97120 0.00080 +HG03953 32 97549873 1614770 29.38 23.55 0.97582 0.00077 +HG03953 33 103813965 1726878 29.40 23.42 0.98060 0.00075 +HG03953 34 109265121 1825735 29.40 23.30 0.98501 0.00073 +HG03953 35 113811544 1918548 29.41 23.12 0.99374 0.00072 +HG03953 36 117388968 2004100 29.41 22.89 1.00642 0.00071 +HG03953 37 119308737 2047906 29.40 22.67 1.01187 0.00071 +HG03953 38 119129563 2066646 29.39 22.26 1.02266 0.00071 +HG03953 39 117112751 2045222 29.38 21.80 1.02949 0.00072 +HG03953 40 113531023 2007535 29.36 21.03 1.04240 0.00074 +HG03953 41 108538915 1911539 29.36 20.90 1.03820 0.00075 +HG03953 42 102636158 1791733 29.36 20.84 1.02910 0.00077 +HG03953 43 96572772 1651660 29.37 21.15 1.00821 0.00078 +HG03953 44 91161017 1515507 29.38 21.77 0.98002 0.00080 +HG03953 45 86813127 1424620 29.40 22.27 0.96738 0.00081 +HG03953 46 83495228 1352343 29.42 22.54 0.95480 0.00082 +HG03953 47 80860980 1299828 29.43 22.73 0.94762 0.00083 +HG03953 48 78209642 1251917 29.43 22.79 0.94363 0.00084 +HG03953 49 74919937 1197204 29.43 22.88 0.94201 0.00086 +HG03953 50 70709108 1127633 29.44 23.07 0.94011 0.00089 +HG03953 51 65735082 1046043 29.44 23.26 0.93807 0.00092 +HG03953 52 60580123 965681 29.44 23.45 0.93970 0.00096 +HG03953 53 55774583 888636 29.44 23.63 0.93923 0.00100 +HG03953 54 51498035 822402 29.44 23.72 0.94141 0.00104 +HG03953 55 47734059 766843 29.45 23.77 0.94703 0.00108 +HG03953 56 44077913 711984 29.43 23.75 0.95221 0.00113 +HG03953 57 40172798 653370 29.43 23.67 0.95877 0.00119 +HG03953 58 35856348 587622 29.39 23.65 0.96609 0.00126 +HG03953 59 31149734 510879 29.41 23.55 0.96683 0.00135 +HG03953 60 26417697 437943 29.41 23.39 0.97725 0.00148 +HG03953 61 22038376 367199 29.40 23.33 0.98222 0.00162 +HG03953 62 18286530 307438 29.38 23.18 0.99109 0.00179 +HG03953 63 15159143 258074 29.36 22.98 1.00359 0.00198 +HG03953 64 12585961 217495 29.34 22.83 1.01870 0.00218 +HG03953 65 10428539 182454 29.30 22.58 1.03137 0.00241 +HG03953 66 8632633 153232 29.25 22.30 1.04638 0.00267 +HG03953 67 7041536 126784 29.21 22.05 1.06141 0.00298 +HG03953 68 5661754 104599 29.12 21.81 1.08908 0.00337 +HG03953 69 4546547 85250 29.04 21.50 1.10535 0.00379 +HG03953 70 3655053 69208 29.08 21.19 1.11621 0.00424 +HG03953 71 2922061 56209 29.06 21.09 1.13397 0.00478 +HG03953 72 2362361 45783 29.07 20.96 1.14247 0.00534 +HG03953 73 1923760 38308 29.00 20.79 1.17388 0.00600 +HG03953 74 1580488 32448 28.96 20.98 1.21027 0.00672 +HG03953 75 1323043 27827 28.98 20.96 1.23987 0.00743 +HG03953 76 1137649 23748 28.90 20.83 1.23056 0.00799 +HG03953 77 997806 21600 28.91 20.73 1.27612 0.00868 +HG03953 78 879855 19449 28.80 20.29 1.30308 0.00934 +HG03953 79 762290 16635 28.73 20.23 1.28643 0.00997 +HG03953 80 647118 13756 28.70 20.05 1.25312 0.01068 +HG03953 81 542500 11615 28.60 20.13 1.26213 0.01171 +HG03953 82 453099 10233 28.54 19.81 1.33136 0.01316 +HG03953 83 370941 8347 28.40 19.57 1.32651 0.01452 +HG03953 84 288967 7368 27.74 19.39 1.50310 0.01751 +HG03953 85 210210 5450 27.95 19.12 1.52837 0.02070 +HG03953 86 140523 3861 28.05 18.88 1.61971 0.02607 +HG03953 87 91803 2735 27.91 18.69 1.75625 0.03358 +HG03953 88 63422 1818 27.88 18.44 1.68982 0.03963 +HG03953 89 41013 1348 27.49 18.19 1.93755 0.05277 +HG03953 90 26697 883 27.84 18.62 1.94977 0.06561 +HG03953 91 17111 1195 24.94 19.79 4.11697 0.11910 +HG03953 92 10191 363 26.92 18.25 2.09979 0.11021 +HG03953 93 6471 314 25.45 18.08 2.86051 0.16143 +HG03953 94 3625 874 19.72 18.96 14.21309 0.48077 +HG03953 95 1715 25406 20.57 15.68 873.28780 5.47885 +HG03953 96 993 3976 23.11 15.61 236.03823 3.74334 +HG03953 97 664 39333 26.17 15.48 3491.99986 17.60742 +HG03953 98 358 26143 20.06 17.01 4304.84601 26.62440 +HG03953 99 158 16826 20.72 15.49 6277.82236 48.39702 +HG03953 100 501 7 18.44 15.03 0.82366 0.31131 diff --git a/data/modules/riker/gcbias/HG03953.gcbias-summary.txt b/data/modules/riker/gcbias/HG03953.gcbias-summary.txt new file mode 100644 index 00000000..29842a38 --- /dev/null +++ b/data/modules/riker/gcbias/HG03953.gcbias-summary.txt @@ -0,0 +1,2 @@ +sample window_size total_clusters aligned_reads at_dropout gc_dropout gc_0_19_normcov gc_20_39_normcov gc_40_59_normcov gc_60_79_normcov gc_80_100_normcov +HG03953 100 25794918 51627320 1.28581 0.78299 1.60739 1.00695 0.97494 1.02991 3.67370 diff --git a/data/modules/riker/hybcap/HG00240.hybcap-metrics.txt b/data/modules/riker/hybcap/HG00240.hybcap-metrics.txt new file mode 100644 index 00000000..e884ba2f --- /dev/null +++ b/data/modules/riker/hybcap/HG00240.hybcap-metrics.txt @@ -0,0 +1,2 @@ +sample panel_name genome_size bait_territory target_territory bait_design_efficiency total_reads deduped_reads deduped_reads_aligned total_bases bases_aligned deduped_bases_aligned on_bait_bases near_bait_bases off_bait_bases on_target_bases on_target_bases_from_pairs selected_pairs selected_unique_pairs frac_deduped_reads frac_deduped_reads_aligned frac_selected_bases frac_off_bait on_bait_vs_selected mean_bait_coverage mean_target_coverage median_target_coverage max_target_coverage min_target_coverage frac_uncovered_targets fold_enrichment fold_80_base_penalty frac_exc_dupe frac_exc_mapq frac_exc_overlap frac_exc_baseq frac_exc_off_target frac_target_bases_1x frac_target_bases_10x frac_target_bases_20x frac_target_bases_30x frac_target_bases_50x frac_target_bases_100x frac_target_bases_250x frac_target_bases_500x frac_target_bases_1000x at_dropout gc_dropout frac_usable_bases_on_bait frac_usable_bases_on_target hs_library_size hs_penalty_10x hs_penalty_20x hs_penalty_30x hs_penalty_40x hs_penalty_50x hs_penalty_100x +HG00240 output_1000G_Exome.v1 3217346917 46106635 46106635 1.000000 98580386 91792601 91581325 9858038600 10643786987 9978299743 4925288538 2365011060 3353487389 3832936583 3830372008 36910710 34275479 0.931145 0.997698 0.684935 0.315065 0.675595 106.82 83.13 69.00 3051 0 0.022314 32.29 3.61 0.062524 0.076124 0.032542 0.053970 0.414730 0.966910 0.888920 0.824546 0.760370 0.629690 0.327539 0.028106 0.001281 0.000048 0.40 19.63 0.499622 0.388813 246041533 9.70 10.03 10.38 10.77 11.21 14.46 diff --git a/data/modules/riker/isize/HG00240.isize-histogram.txt b/data/modules/riker/isize/HG00240.isize-histogram.txt new file mode 100644 index 00000000..bca51420 --- /dev/null +++ b/data/modules/riker/isize/HG00240.isize-histogram.txt @@ -0,0 +1,742 @@ +sample insert_size fr_count rf_count tandem_count +HG00240 1 0 3 19 +HG00240 2 18 6 12 +HG00240 3 28 9 6 +HG00240 4 41 4 5 +HG00240 5 36 4 9 +HG00240 6 37 3 11 +HG00240 7 35 8 10 +HG00240 8 39 4 2 +HG00240 9 41 5 3 +HG00240 10 33 5 3 +HG00240 11 41 3 4 +HG00240 12 32 3 4 +HG00240 13 48 6 3 +HG00240 14 40 7 1 +HG00240 15 47 3 0 +HG00240 16 41 2 0 +HG00240 17 41 5 1 +HG00240 18 52 3 2 +HG00240 19 121 4 2 +HG00240 20 92 5 1 +HG00240 21 74 3 1 +HG00240 22 73 5 2 +HG00240 23 81 8 1 +HG00240 24 90 2 1 +HG00240 25 84 10 0 +HG00240 26 71 4 1 +HG00240 27 61 8 0 +HG00240 28 70 4 1 +HG00240 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+HG00240 732 244 2 2 +HG00240 733 252 2 5 +HG00240 734 211 3 1 +HG00240 735 226 3 3 +HG00240 736 214 3 2 +HG00240 737 223 3 4 +HG00240 738 210 2 3 +HG00240 739 204 1 2 +HG00240 740 227 1 1 +HG00240 741 187 4 2 diff --git a/data/modules/riker/isize/HG00240.isize-metrics.txt b/data/modules/riker/isize/HG00240.isize-metrics.txt new file mode 100644 index 00000000..05eb883e --- /dev/null +++ b/data/modules/riker/isize/HG00240.isize-metrics.txt @@ -0,0 +1,2 @@ +sample pair_orientation read_pairs mean_insert_size standard_deviation median_insert_size median_absolute_deviation mode_insert_size min_insert_size max_insert_size +HG00240 FR 44718990 253.40 80.08 241.00 50.00 212 2 247959841 diff --git a/data/modules/riker/isize/HG03953.isize-histogram.txt b/data/modules/riker/isize/HG03953.isize-histogram.txt new file mode 100644 index 00000000..510909bc --- /dev/null +++ b/data/modules/riker/isize/HG03953.isize-histogram.txt @@ -0,0 +1,1087 @@ +sample insert_size fr_count rf_count tandem_count 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b/data/modules/riker/isize/HG03953.isize-metrics.txt @@ -0,0 +1,2 @@ +sample pair_orientation read_pairs mean_insert_size standard_deviation median_insert_size median_absolute_deviation mode_insert_size min_insert_size max_insert_size +HG03953 FR 22666326 435.34 102.64 426.00 66.00 399 2 231498245 diff --git a/data/modules/riker/wgs/HG03953.wgs-coverage.txt b/data/modules/riker/wgs/HG03953.wgs-coverage.txt new file mode 100644 index 00000000..0e25a0de --- /dev/null +++ b/data/modules/riker/wgs/HG03953.wgs-coverage.txt @@ -0,0 +1,252 @@ +sample depth bases frac_bases bases_at_or_above frac_bases_at_or_above +HG03953 0 544461140 0.17890 3043453562 1.00000 +HG03953 1 701573680 0.23052 2498992422 0.82110 +HG03953 2 737951772 0.24247 1797418742 0.59059 +HG03953 3 538916709 0.17707 1059466970 0.34811 +HG03953 4 301918141 0.09920 520550261 0.17104 +HG03953 5 137550393 0.04520 218632120 0.07184 +HG03953 6 53150615 0.01746 81081727 0.02664 +HG03953 7 18081118 0.00594 27931112 0.00918 +HG03953 8 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frac_excluded_unpaired frac_excluded_baseq frac_excluded_overlap frac_excluded_capped frac_excluded_total frac_bases_at_1x frac_bases_at_5x frac_bases_at_10x frac_bases_at_15x frac_bases_at_20x frac_bases_at_25x frac_bases_at_30x frac_bases_at_40x frac_bases_at_50x frac_bases_at_60x frac_bases_at_100x fold_80_base_penalty fold_90_base_penalty fold_95_base_penalty +HG03953 3043453562 2.06 2.10 2.00 1.00 0.05880 0.08244 0.00091 0.01497 0.00666 0.00472 0.16850 0.82110 0.07184 0.00079 0.00031 0.00022 0.00017 0.00013 0.00009 0.00007 0.00006 0.00004 2.06 0.00 0.00