From 2297ffa3a57822933838aa420210b9198e838407 Mon Sep 17 00:00:00 2001 From: saramonzon Date: Wed, 8 Aug 2018 15:45:23 +0200 Subject: [PATCH] Added --version to main.nf --- .circleci/config.yml | 9 +- .gitignore | 2 +- Dockerfile | 1 + main.nf | 13 +- nextflow.config | 2 +- results/bwa/A.sorted.bam | Bin 2242419 -> 2242419 bytes results/bwa/A.stats.txt | 578 +++++++++++++++++++++++---------------- results/bwa/B.sorted.bam | Bin 2245374 -> 2245374 bytes results/bwa/B.stats.txt | 578 +++++++++++++++++++++++---------------- results/bwa/C.sorted.bam | Bin 2245374 -> 2245374 bytes results/bwa/C.stats.txt | 578 +++++++++++++++++++++++---------------- results/report.html | 23 +- results/timeline.html | 26 +- results/trace.txt | 10 - results/vcf/A.vcf | 465 +++++++++++++++---------------- results/vcf/B.vcf | 524 +++++++++++++++++------------------ results/vcf/C.vcf | 524 +++++++++++++++++------------------ 17 files changed, 1807 insertions(+), 1526 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index d82f7a9..2025068 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -22,8 +22,13 @@ jobs: working_directory: /tmp/src steps: - run: - name: Install parallel gzip and python3 - command: apk add --no-cache pigz python3 + name: Install parallel gzip, python3 and java + command: apk add --no-cache pigz python3 java + - run: + name: Install nextflow + command: | + wget -qO- https://get.nextflow.io | bash + export PATH=$PATH:$PWD/nextflow - restore_cache: keys: - docker-v1-{{ .Branch }}-{{ epoch }} diff --git a/.gitignore b/.gitignore index d2afc69..fd46b55 100644 --- a/.gitignore +++ b/.gitignore @@ -11,4 +11,4 @@ work/ nextflow # Ignore results files -results +results/ diff --git a/Dockerfile b/Dockerfile index 27d774e..d1d0a93 100644 --- a/Dockerfile +++ b/Dockerfile @@ -21,3 +21,4 @@ ENV PATH=${PATH}:/scif/apps/bcftools/bin # SciF Entrypoint # Disabled because of compatibility with nextflow. #ENTRYPOINT ["scif"] +CMD scif diff --git a/main.nf b/main.nf index 6803896..d426b6a 100644 --- a/main.nf +++ b/main.nf @@ -22,7 +22,7 @@ Pipeline overview: def helpMessage() { log.info""" ========================================= - BU-ISCIII/nextflow-scif DEMO PIPELINE v${version} + BU-ISCIII/nextflow-scif DEMO PIPELINE v${params.ver} ========================================= Usage: @@ -36,13 +36,11 @@ def helpMessage() { --outdir Output dir. --help show this message. -profile Hardware config to use. standard/docker/singularity. Default: standard. + --version Show pipeline version. """.stripIndent() } -// Pipeline version -version = '0.1' - // Show help message params.help = false if (params.help){ @@ -50,6 +48,13 @@ if (params.help){ exit 0 } +if (params.version){ + log.info""" + v${params.ver} + """.stripIndent() + exit 0 +} + // Default parameters params.reads = "$baseDir/data/samples/*.fastq" params.genome = "$baseDir/data/genome.fa" diff --git a/nextflow.config b/nextflow.config index b0caef0..513d2ac 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,7 +16,7 @@ manifest { // Global default params, used in configs params { - version = '0.1' //Pipeline version + ver = '1.1' //Pipeline version nf_required_version = '0.27.6' //Minimum version of Nextflow required reads="$baseDir/data/samples/*.fastq" diff --git a/results/bwa/A.sorted.bam b/results/bwa/A.sorted.bam index 152daaf90b9dbd40ec92368b77ca56419cf39752..b76d3c70b2f00f54dfcd641b8a39afd4a6442d21 100644 GIT binary patch delta 137 zcmWN=xe);Y06@`M*1GTeK89oqpaL3EiQpR}+Mh^OAyI%r1VYI+z?*sL_Y$Q4$vXJB z+2s$<{W*HwJjP)X->)Yzzzk+F#2iML#{w3ygk`K?6>C_>1~##UZR}tdd)UVT4snEI QoZu8^IL8GpAFkfpA0I+DF8}}l delta 137 zcmWN=ISv5<06@_U!`OFYUqj;noIvFmN~ci#iPEo~LnCn+5~XG?z)N2Gy#(q1brrl_ z@1oCRpCobYaT7jor^8tcFoRhPF^74Kuz*D@VHqn}#TwSJflX{-8#~y=7<<^q0S&e%@Nv10 zchBu9dfnWw!uR=mKZ*gSFpVK*Fv1wKn8Q34u!torV+E^N!#Xywi7jkn2fNtAJ`Qk* OBOK!dr#O2!KWu(4xHlRA delta 137 zcmWN=Ne;mP06@`{Qu9=5ri6_Hu$MTAwT&BC{3dq(VQgGS;uacS@^bD${{PqnZ?}i& z^Ezc&l6c;Q-+g?&i2)X{h#{7+j1g9_iZ!fb1Dn{wHg>R!J&duB159v;BOK!dr#Qno NE^vt{uAZ(h#~-InHO>G4 diff --git a/results/bwa/B.stats.txt b/results/bwa/B.stats.txt index 30dbb51..6d0271f 100644 --- a/results/bwa/B.stats.txt +++ b/results/bwa/B.stats.txt @@ -1,17 +1,16 @@ -# This file was produced by samtools stats (1.9+htslib-1.9) and can be plotted using plot-bamstats -# This file contains statistics for all reads. +# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats # The command line was: stats B.sorted.bam # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) CHK 95d7cf2e 356c45e0 861b8a9a # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. -SN raw total sequences: 25000 +SN raw total sequences: 25001 SN filtered sequences: 0 -SN sequences: 25000 +SN sequences: 25001 SN is sorted: 1 -SN 1st fragments: 25000 +SN 1st fragments: 25001 SN last fragments: 0 -SN reads mapped: 500 +SN reads mapped: 501 SN reads mapped and paired: 0 # paired-end technology bit set + both mates mapped SN reads unmapped: 24500 SN reads properly paired: 0 # proper-pair bit set @@ -20,21 +19,15 @@ SN reads duplicated: 0 # PCR or optical duplicate bit set SN reads MQ0: 4 # mapped and MQ=0 SN reads QC failed: 0 SN non-primary alignments: 1 -SN total length: 2525000 # ignores clipping -SN total first fragment length: 2525000 # ignores clipping -SN total last fragment length: 0 # ignores clipping -SN bases mapped: 50500 # ignores clipping -SN bases mapped (cigar): 47348 # more accurate +SN total length: 2525042 # ignores clipping +SN bases mapped: 50542 # ignores clipping +SN bases mapped (cigar): 47390 # more accurate SN bases trimmed: 0 SN bases duplicated: 0 -SN mismatches: 1107 # from NM fields -SN error rate: 2.338008e-02 # mismatches / bases mapped (cigar) -SN average length: 101 -SN average first fragment length: 101 -SN average last fragment length: 0 +SN mismatches: 1109 # from NM fields +SN error rate: 2.340156e-02 # mismatches / bases mapped (cigar) +SN average length: 100 SN maximum length: 101 -SN maximum first fragment length: 0 -SN maximum last fragment length: 0 SN average quality: 31.0 SN insert size average: 0.0 SN insert size standard deviation: 0.0 @@ -42,11 +35,214 @@ SN inward oriented pairs: 0 SN outward oriented pairs: 0 SN pairs with other orientation: 0 SN pairs on different chromosomes: 0 -SN percentage of properly paired reads (%): 0.0 -# First Fragment Qualities. Use `grep ^FFQ | cut -f 2-` to extract this part. +# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part. # Columns correspond to qualities and rows to cycles. First column is the cycle number. -# Last Fragment Qualities. Use `grep ^LFQ | cut -f 2-` to extract this part. +FFQ 1 0 0 278 0 0 0 0 0 0 0 818 0 0 0 0 0 690 0 0 0 0 0 41 446 1 592 768 690 951 0 2526 8981 0 2808 5411 0 0 0 0 0 0 0 0 +FFQ 2 0 0 278 0 0 0 0 0 0 0 787 0 0 0 0 0 700 0 0 0 0 0 78 385 1 593 732 822 794 0 2119 8398 0 2180 7134 0 0 0 0 0 0 0 0 +FFQ 3 0 0 287 0 0 0 0 0 0 0 942 0 0 0 0 0 791 0 0 0 0 0 148 428 0 519 748 1021 723 0 1991 8332 0 1699 7371 1 0 0 0 0 0 0 0 +FFQ 4 0 0 300 0 0 0 0 0 0 0 702 0 0 0 0 0 212 0 0 521 0 0 86 0 0 377 295 21 686 0 664 12 1157 1554 0 6976 0 11437 1 0 0 0 0 +FFQ 5 0 0 331 0 0 0 0 0 0 0 695 0 0 0 0 0 203 0 0 451 0 0 90 0 0 406 355 18 740 0 704 5 1129 1508 0 6790 0 11576 0 0 0 0 0 +FFQ 6 0 0 363 0 0 0 0 0 122 0 632 331 0 0 1 43 50 412 121 188 0 11 8 186 0 464 413 65 496 242 866 104 1351 1529 0 6013 586 10404 0 0 0 0 0 +FFQ 7 0 0 379 0 0 0 0 0 92 1 555 263 0 0 0 55 40 531 86 140 0 6 11 130 1 407 341 65 601 160 742 113 1269 1440 0 6232 684 10657 0 0 0 0 0 +FFQ 8 0 0 397 0 0 1 2 0 66 0 349 184 0 0 0 43 26 451 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130 743 430 488 950 717 764 1609 1342 1660 1537 1933 2469 2492 2296 0 +FFQ 66 0 0 2938 0 0 3 40 156 311 19 11 26 35 173 54 6 13 28 134 112 104 100 355 218 85 145 631 136 654 493 433 976 682 720 1624 1444 1781 1492 1839 2344 2401 2284 0 +FFQ 67 0 0 2989 0 0 3 30 131 260 15 5 26 47 176 38 13 20 23 111 114 139 109 328 211 68 166 615 106 720 494 477 929 738 703 1703 1601 1757 1518 1763 2464 2166 2224 0 +FFQ 68 0 0 3040 0 0 2 35 96 195 11 5 34 26 128 33 6 17 19 116 107 117 89 330 155 65 141 667 138 650 511 477 954 740 704 1743 1676 1955 1655 1692 2424 2110 2137 0 +FFQ 69 0 0 3099 0 0 0 34 125 209 6 1 23 24 145 25 10 14 23 161 75 127 105 329 142 52 129 651 123 604 541 494 1010 797 771 1802 1810 1887 1767 1654 2341 1999 1891 0 +FFQ 70 0 0 3154 0 0 2 33 130 194 5 10 32 29 138 33 4 14 25 144 89 131 112 320 129 100 158 665 113 598 547 504 951 811 716 1914 2100 1935 1787 1443 2357 1817 1756 0 +FFQ 71 0 0 3223 0 0 4 29 135 180 8 6 28 24 129 26 7 18 21 146 64 134 117 291 120 105 194 696 126 536 593 563 981 792 757 1998 2169 2061 1819 1401 2278 1682 1539 0 +FFQ 72 0 0 3290 0 0 5 40 141 191 4 9 27 24 131 41 9 25 27 175 97 169 131 300 114 106 176 733 125 527 673 570 1010 885 748 2055 2234 2045 1815 1276 2176 1504 1392 0 +FFQ 73 0 0 3386 0 0 8 41 189 224 4 10 40 37 131 24 9 22 32 190 75 165 133 312 111 119 207 783 130 498 710 583 996 878 864 2184 2377 2084 1728 1171 2034 1313 1198 0 +FFQ 74 0 0 3474 0 0 4 53 248 219 3 12 38 31 149 31 15 18 35 206 83 199 127 291 113 121 225 797 158 478 753 592 1113 884 852 2160 2427 2149 1737 1069 1979 1153 1004 0 +FFQ 75 0 0 3563 0 0 7 55 249 239 5 15 61 38 158 33 11 23 37 237 68 204 171 298 111 144 233 907 150 479 830 643 1041 917 842 2364 2507 2123 1661 947 1784 970 875 0 +FFQ 76 0 0 3647 0 0 13 113 589 462 5 36 87 48 204 39 17 29 77 390 134 289 171 381 140 174 370 1029 198 481 976 666 1195 969 907 2351 2264 1848 1355 773 1269 762 542 0 +FFQ 77 0 0 3704 0 0 9 61 358 241 1 27 119 56 235 36 18 18 41 251 92 350 199 385 137 186 312 1083 157 538 922 735 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1147 1060 3257 3486 1839 1215 332 764 355 273 0 +FFQ 84 0 0 4189 0 0 12 20 268 74 0 40 65 43 79 20 25 9 46 223 69 326 132 139 150 176 392 910 219 270 1093 696 1290 1129 1037 3435 3904 1794 1152 283 714 321 256 0 +FFQ 85 0 0 4267 0 0 13 21 254 59 0 23 50 33 69 14 30 15 59 204 57 256 114 106 135 173 410 767 208 226 1108 711 1314 1209 1029 3591 4117 1829 1131 265 613 269 251 0 +FFQ 86 0 0 4367 0 0 11 27 308 62 0 28 63 35 51 17 27 32 45 227 83 323 112 104 145 213 471 754 273 217 1103 680 1314 1205 1047 3609 4142 1728 1011 217 517 249 183 0 +FFQ 87 0 0 4480 0 0 16 21 304 48 0 36 74 34 41 22 25 24 63 253 71 395 107 97 157 203 469 747 246 209 1128 636 1397 1193 1045 3692 4185 1650 899 230 422 223 158 0 +FFQ 88 0 0 4593 0 0 18 28 314 41 0 34 71 32 43 15 25 22 40 239 104 362 92 91 154 195 502 732 279 198 1115 670 1387 1242 1069 3737 4277 1505 796 186 425 210 157 0 +FFQ 89 0 0 4701 0 0 23 22 331 46 0 43 74 44 36 17 38 21 63 272 109 364 80 80 158 194 569 715 279 157 1180 646 1322 1196 1115 3679 4404 1443 720 171 370 164 154 0 +FFQ 90 0 0 4819 0 0 18 20 265 28 0 44 74 41 34 18 25 16 59 222 120 375 71 51 170 218 555 644 314 175 1174 635 1381 1279 1066 3885 4390 1383 643 153 320 158 157 0 +FFQ 91 0 0 4976 0 0 20 23 295 33 0 42 68 38 15 15 37 14 72 285 110 351 71 58 185 214 554 601 317 159 1129 621 1440 1262 1025 3813 4572 1343 549 124 296 139 134 0 +FFQ 92 0 0 5115 0 0 23 22 344 24 0 60 74 36 20 14 38 28 64 294 118 349 57 41 199 234 610 590 349 138 1144 664 1412 1239 1040 3807 4502 1248 519 104 256 124 100 0 +FFQ 93 0 0 5260 0 0 23 20 270 34 0 61 64 32 17 10 41 24 79 240 140 357 50 46 178 177 676 467 325 136 1212 660 1345 1271 1123 3797 4654 1183 468 112 227 126 95 0 +FFQ 94 0 0 5439 0 0 17 14 234 22 0 38 46 25 11 13 29 14 64 212 139 333 47 35 173 206 603 395 348 125 1131 664 1412 1307 1014 4011 4800 1139 417 81 240 107 95 0 +FFQ 95 0 0 5668 0 0 13 9 184 16 0 33 29 19 23 10 38 15 46 253 135 279 31 35 157 214 632 382 391 117 1126 592 1419 1296 1070 3942 4924 1058 371 77 221 90 85 0 +FFQ 96 0 0 5930 0 0 17 8 160 12 0 24 24 10 19 4 28 13 60 194 144 280 24 29 162 194 604 344 405 87 1100 678 1392 1290 1099 4022 4853 1031 339 63 226 67 64 0 +FFQ 97 0 0 6297 0 0 16 5 154 6 0 28 33 7 20 2 33 17 55 228 126 253 18 22 195 211 706 333 378 98 1207 661 1447 1328 1009 3955 4530 949 318 44 210 51 50 0 +FFQ 98 0 0 6632 0 0 8 1 109 9 0 25 15 5 13 2 26 19 56 214 135 225 20 21 159 211 673 293 413 73 1204 667 1497 1297 1009 4027 4430 900 310 52 171 46 33 0 +FFQ 99 0 0 7043 0 0 1 0 32 3 0 15 4 1 0 1 27 12 40 205 131 193 16 28 158 212 689 270 371 62 1168 602 1422 1358 1051 4017 4487 842 281 40 171 26 21 0 +FFQ 100 0 0 7465 0 0 0 0 0 0 0 0 0 0 0 0 17 12 40 169 112 177 9 19 111 169 616 205 353 51 1131 625 1496 1379 1087 4095 4381 766 277 48 162 14 14 0 +FFQ 101 0 0 8027 0 0 0 0 0 0 0 0 0 0 0 0 67 46 85 547 254 323 18 50 241 344 1172 346 565 88 1734 736 1795 1570 909 3625 1908 329 121 15 82 2 1 0 +FFQ 102 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +# Last Fragment Qualitites. Use `grep ^LFQ | cut -f 2-` to extract this part. # Columns correspond to qualities and rows to cycles. First column is the cycle number. +LFQ 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 66 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 68 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 69 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 71 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 72 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 73 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 74 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 75 0 0 0 0 0 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0 0 0 0 0 0 0 0 +LFQ 86 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 87 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 88 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 89 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 90 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 91 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 92 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 93 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 96 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 97 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 98 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 99 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 101 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 102 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. GCF 0.25 10 GCF 1.01 50 @@ -68,9 +264,10 @@ GCF 16.08 73 GCF 17.09 59 GCF 18.59 72 GCF 20.10 66 -GCF 21.11 85 -GCF 22.11 105 -GCF 23.12 132 +GCF 20.85 85 +GCF 21.36 86 +GCF 22.11 106 +GCF 23.12 133 GCF 24.12 146 GCF 25.13 176 GCF 26.13 225 @@ -130,216 +327,111 @@ GCF 85.43 1 GCF 88.94 0 GCF 92.46 1 # GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. -# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] -GCC 1 33.85 17.65 18.44 30.06 0.00 0.00 -GCC 2 35.07 16.30 17.58 31.05 0.00 0.00 -GCC 3 32.25 17.26 17.67 32.82 0.00 0.00 -GCC 4 31.53 17.94 18.41 32.12 0.00 0.00 -GCC 5 32.47 17.01 18.72 31.80 0.00 0.00 -GCC 6 31.93 19.23 18.60 30.24 0.04 0.00 -GCC 7 32.05 17.49 19.16 31.30 0.00 0.00 -GCC 8 31.60 18.49 18.32 31.59 0.01 0.00 -GCC 9 31.46 18.40 17.96 32.18 0.01 0.00 -GCC 10 32.14 18.01 18.87 30.98 0.00 0.00 -GCC 11 32.02 17.56 17.86 32.56 0.01 0.00 -GCC 12 32.06 17.61 18.01 32.32 0.04 0.00 -GCC 13 31.86 17.67 18.59 31.88 0.00 0.00 -GCC 14 31.72 17.68 18.44 32.16 0.00 0.00 -GCC 15 31.64 18.03 17.99 32.34 0.03 0.00 -GCC 16 32.04 17.73 18.49 31.74 0.05 0.00 -GCC 17 32.02 18.40 18.02 31.56 0.06 0.00 -GCC 18 31.63 18.35 18.24 31.78 0.05 0.00 -GCC 19 31.85 18.22 17.94 31.99 0.04 0.00 -GCC 20 32.12 18.23 17.93 31.72 0.07 0.00 -GCC 21 31.18 18.81 18.19 31.82 0.08 0.00 -GCC 22 32.01 18.42 18.27 31.30 0.08 0.00 -GCC 23 31.18 18.35 18.56 31.91 0.09 0.00 -GCC 24 31.38 18.49 18.53 31.60 0.03 0.00 -GCC 25 31.50 18.67 18.32 31.51 0.10 0.00 -GCC 26 31.91 18.42 18.17 31.51 0.10 0.00 -GCC 27 31.81 18.95 18.32 30.92 0.09 0.00 -GCC 28 31.19 18.51 18.96 31.34 0.08 0.00 -GCC 29 30.97 18.35 19.02 31.66 0.08 0.00 -GCC 30 31.43 18.63 18.08 31.85 0.08 0.00 -GCC 31 31.71 18.57 18.62 31.10 0.10 0.00 -GCC 32 30.97 18.49 18.66 31.88 0.10 0.00 -GCC 33 31.35 18.80 18.16 31.69 0.13 0.00 -GCC 34 31.33 18.81 18.36 31.50 0.10 0.00 -GCC 35 31.06 18.45 18.84 31.65 0.10 0.00 -GCC 36 31.38 18.63 18.88 31.10 0.08 0.00 -GCC 37 31.29 18.68 18.52 31.51 0.07 0.00 -GCC 38 31.05 18.63 18.68 31.63 0.04 0.00 -GCC 39 30.99 18.79 18.84 31.38 0.05 0.00 -GCC 40 31.73 17.98 18.61 31.68 0.00 0.00 -GCC 41 31.02 18.70 18.78 31.50 0.00 0.00 -GCC 42 31.40 18.72 18.70 31.17 0.00 0.00 -GCC 43 31.56 18.47 19.10 30.86 0.02 0.00 -GCC 44 30.82 18.22 19.46 31.51 0.00 0.00 -GCC 45 31.24 18.89 18.40 31.47 0.01 0.00 -GCC 46 31.46 19.30 18.58 30.66 0.00 0.00 -GCC 47 31.54 18.24 18.77 31.45 0.00 0.00 -GCC 48 31.80 18.02 18.47 31.72 0.01 0.00 -GCC 49 31.58 18.53 18.27 31.62 0.06 0.00 -GCC 50 31.38 18.37 18.74 31.51 0.04 0.00 -GCC 51 30.59 18.60 18.77 32.04 0.04 0.00 -GCC 52 31.09 18.65 18.81 31.45 0.07 0.00 -GCC 53 31.64 18.61 18.19 31.56 0.08 0.00 -GCC 54 31.01 18.95 18.47 31.57 0.07 0.00 -GCC 55 31.18 18.83 19.04 30.94 0.00 0.00 -GCC 56 32.06 18.78 18.29 30.87 0.00 0.00 -GCC 57 31.92 18.31 18.75 31.02 0.00 0.00 -GCC 58 31.02 18.81 18.38 31.79 0.01 0.00 -GCC 59 31.61 18.11 18.41 31.87 0.00 0.00 -GCC 60 31.44 18.79 18.67 31.10 0.00 0.00 -GCC 61 31.69 18.24 18.63 31.44 0.00 0.00 -GCC 62 31.42 18.27 18.80 31.51 0.00 0.00 -GCC 63 31.65 18.55 18.45 31.35 0.00 0.00 -GCC 64 31.01 18.92 18.45 31.62 0.00 0.00 -GCC 65 31.64 18.14 18.19 32.03 0.00 0.00 -GCC 66 31.36 18.73 18.23 31.68 0.00 0.00 -GCC 67 31.38 18.32 18.30 32.00 0.00 0.00 -GCC 68 31.42 18.17 18.58 31.83 0.00 0.00 -GCC 69 30.92 19.26 18.48 31.34 0.00 0.00 -GCC 70 31.47 18.60 18.31 31.62 0.00 0.00 -GCC 71 31.47 18.52 18.42 31.59 0.00 0.00 -GCC 72 31.45 18.84 18.74 30.96 0.00 0.00 -GCC 73 31.62 18.20 18.52 31.65 0.00 0.00 -GCC 74 31.49 18.05 18.87 31.59 0.00 0.00 -GCC 75 31.45 18.36 18.47 31.72 0.04 0.00 -GCC 76 31.74 18.42 18.44 31.41 0.08 0.00 -GCC 77 31.88 17.98 18.45 31.69 0.07 0.00 -GCC 78 31.27 18.83 18.46 31.44 0.04 0.00 -GCC 79 31.52 18.79 17.95 31.75 0.07 0.00 -GCC 80 31.25 18.62 18.49 31.63 0.07 0.00 -GCC 81 31.68 18.50 18.38 31.44 0.04 0.00 -GCC 82 31.49 18.40 18.47 31.64 0.00 0.00 -GCC 83 31.50 18.67 18.08 31.75 0.00 0.00 -GCC 84 31.56 17.94 18.46 32.03 0.00 0.00 -GCC 85 31.56 18.77 18.20 31.46 0.00 0.00 -GCC 86 31.68 18.16 18.38 31.78 0.00 0.00 -GCC 87 30.95 18.35 19.10 31.60 0.00 0.00 -GCC 88 31.92 18.89 18.31 30.87 0.04 0.00 -GCC 89 31.82 18.47 18.53 31.18 0.03 0.00 -GCC 90 31.64 18.60 18.54 31.22 0.00 0.00 -GCC 91 31.78 18.67 18.18 31.36 0.06 0.00 -GCC 92 32.15 18.27 18.43 31.15 0.10 0.00 -GCC 93 31.25 18.21 18.62 31.91 0.10 0.00 -GCC 94 31.10 18.65 18.63 31.62 0.10 0.00 -GCC 95 31.50 18.24 18.28 31.98 0.11 0.00 -GCC 96 31.38 18.73 18.68 31.21 0.10 0.00 -GCC 97 31.66 18.38 18.11 31.85 0.10 0.00 -GCC 98 31.86 18.24 18.44 31.46 0.10 0.00 -GCC 99 31.63 18.13 18.46 31.77 0.10 0.00 -GCC 100 31.07 18.98 18.52 31.43 0.10 0.00 -GCC 101 31.77 18.59 18.77 30.87 0.10 0.00 -# ACGT content per cycle for first fragments. Use `grep ^FBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] -# ACGT content per cycle for last fragments. Use `grep ^LBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] -LBC 1 33.85 17.65 18.44 30.06 0.00 0.00 -LBC 2 35.07 16.30 17.58 31.05 0.00 0.00 -LBC 3 32.25 17.26 17.67 32.82 0.00 0.00 -LBC 4 31.53 17.94 18.41 32.12 0.00 0.00 -LBC 5 32.47 17.01 18.72 31.80 0.00 0.00 -LBC 6 31.93 19.23 18.60 30.24 0.04 0.00 -LBC 7 32.05 17.49 19.16 31.30 0.00 0.00 -LBC 8 31.60 18.49 18.32 31.59 0.01 0.00 -LBC 9 31.46 18.40 17.96 32.18 0.01 0.00 -LBC 10 32.14 18.01 18.87 30.98 0.00 0.00 -LBC 11 32.02 17.56 17.86 32.56 0.01 0.00 -LBC 12 32.06 17.61 18.01 32.32 0.04 0.00 -LBC 13 31.86 17.67 18.59 31.88 0.00 0.00 -LBC 14 31.72 17.68 18.44 32.16 0.00 0.00 -LBC 15 31.64 18.03 17.99 32.34 0.03 0.00 -LBC 16 32.04 17.73 18.49 31.74 0.05 0.00 -LBC 17 32.02 18.40 18.02 31.56 0.06 0.00 -LBC 18 31.63 18.35 18.24 31.78 0.05 0.00 -LBC 19 31.85 18.22 17.94 31.99 0.04 0.00 -LBC 20 32.12 18.23 17.93 31.72 0.07 0.00 -LBC 21 31.18 18.81 18.19 31.82 0.08 0.00 -LBC 22 32.01 18.42 18.27 31.30 0.08 0.00 -LBC 23 31.18 18.35 18.56 31.91 0.09 0.00 -LBC 24 31.38 18.49 18.53 31.60 0.03 0.00 -LBC 25 31.50 18.67 18.32 31.51 0.10 0.00 -LBC 26 31.91 18.42 18.17 31.51 0.10 0.00 -LBC 27 31.81 18.95 18.32 30.92 0.09 0.00 -LBC 28 31.19 18.51 18.96 31.34 0.08 0.00 -LBC 29 30.97 18.35 19.02 31.66 0.08 0.00 -LBC 30 31.43 18.63 18.08 31.85 0.08 0.00 -LBC 31 31.71 18.57 18.62 31.10 0.10 0.00 -LBC 32 30.97 18.49 18.66 31.88 0.10 0.00 -LBC 33 31.35 18.80 18.16 31.69 0.13 0.00 -LBC 34 31.33 18.81 18.36 31.50 0.10 0.00 -LBC 35 31.06 18.45 18.84 31.65 0.10 0.00 -LBC 36 31.38 18.63 18.88 31.10 0.08 0.00 -LBC 37 31.29 18.68 18.52 31.51 0.07 0.00 -LBC 38 31.05 18.63 18.68 31.63 0.04 0.00 -LBC 39 30.99 18.79 18.84 31.38 0.05 0.00 -LBC 40 31.73 17.98 18.61 31.68 0.00 0.00 -LBC 41 31.02 18.70 18.78 31.50 0.00 0.00 -LBC 42 31.40 18.72 18.70 31.17 0.00 0.00 -LBC 43 31.56 18.47 19.10 30.86 0.02 0.00 -LBC 44 30.82 18.22 19.46 31.51 0.00 0.00 -LBC 45 31.24 18.89 18.40 31.47 0.01 0.00 -LBC 46 31.46 19.30 18.58 30.66 0.00 0.00 -LBC 47 31.54 18.24 18.77 31.45 0.00 0.00 -LBC 48 31.80 18.02 18.47 31.72 0.01 0.00 -LBC 49 31.58 18.53 18.27 31.62 0.06 0.00 -LBC 50 31.38 18.37 18.74 31.51 0.04 0.00 -LBC 51 30.59 18.60 18.77 32.04 0.04 0.00 -LBC 52 31.09 18.65 18.81 31.45 0.07 0.00 -LBC 53 31.64 18.61 18.19 31.56 0.08 0.00 -LBC 54 31.01 18.95 18.47 31.57 0.07 0.00 -LBC 55 31.18 18.83 19.04 30.94 0.00 0.00 -LBC 56 32.06 18.78 18.29 30.87 0.00 0.00 -LBC 57 31.92 18.31 18.75 31.02 0.00 0.00 -LBC 58 31.02 18.81 18.38 31.79 0.01 0.00 -LBC 59 31.61 18.11 18.41 31.87 0.00 0.00 -LBC 60 31.44 18.79 18.67 31.10 0.00 0.00 -LBC 61 31.69 18.24 18.63 31.44 0.00 0.00 -LBC 62 31.42 18.27 18.80 31.51 0.00 0.00 -LBC 63 31.65 18.55 18.45 31.35 0.00 0.00 -LBC 64 31.01 18.92 18.45 31.62 0.00 0.00 -LBC 65 31.64 18.14 18.19 32.03 0.00 0.00 -LBC 66 31.36 18.73 18.23 31.68 0.00 0.00 -LBC 67 31.38 18.32 18.30 32.00 0.00 0.00 -LBC 68 31.42 18.17 18.58 31.83 0.00 0.00 -LBC 69 30.92 19.26 18.48 31.34 0.00 0.00 -LBC 70 31.47 18.60 18.31 31.62 0.00 0.00 -LBC 71 31.47 18.52 18.42 31.59 0.00 0.00 -LBC 72 31.45 18.84 18.74 30.96 0.00 0.00 -LBC 73 31.62 18.20 18.52 31.65 0.00 0.00 -LBC 74 31.49 18.05 18.87 31.59 0.00 0.00 -LBC 75 31.45 18.36 18.47 31.72 0.04 0.00 -LBC 76 31.74 18.42 18.44 31.41 0.08 0.00 -LBC 77 31.88 17.98 18.45 31.69 0.07 0.00 -LBC 78 31.27 18.83 18.46 31.44 0.04 0.00 -LBC 79 31.52 18.79 17.95 31.75 0.07 0.00 -LBC 80 31.25 18.62 18.49 31.63 0.07 0.00 -LBC 81 31.68 18.50 18.38 31.44 0.04 0.00 -LBC 82 31.49 18.40 18.47 31.64 0.00 0.00 -LBC 83 31.50 18.67 18.08 31.75 0.00 0.00 -LBC 84 31.56 17.94 18.46 32.03 0.00 0.00 -LBC 85 31.56 18.77 18.20 31.46 0.00 0.00 -LBC 86 31.68 18.16 18.38 31.78 0.00 0.00 -LBC 87 30.95 18.35 19.10 31.60 0.00 0.00 -LBC 88 31.92 18.89 18.31 30.87 0.04 0.00 -LBC 89 31.82 18.47 18.53 31.18 0.03 0.00 -LBC 90 31.64 18.60 18.54 31.22 0.00 0.00 -LBC 91 31.78 18.67 18.18 31.36 0.06 0.00 -LBC 92 32.15 18.27 18.43 31.15 0.10 0.00 -LBC 93 31.25 18.21 18.62 31.91 0.10 0.00 -LBC 94 31.10 18.65 18.63 31.62 0.10 0.00 -LBC 95 31.50 18.24 18.28 31.98 0.11 0.00 -LBC 96 31.38 18.73 18.68 31.21 0.10 0.00 -LBC 97 31.66 18.38 18.11 31.85 0.10 0.00 -LBC 98 31.86 18.24 18.44 31.46 0.10 0.00 -LBC 99 31.63 18.13 18.46 31.77 0.10 0.00 -LBC 100 31.07 18.98 18.52 31.43 0.10 0.00 -LBC 101 31.77 18.59 18.77 30.87 0.10 0.00 +# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle, and A,C,G,T counts [%] +GCC 1 33.85 17.65 18.44 30.06 +GCC 2 35.07 16.30 17.59 31.05 +GCC 3 32.25 17.26 17.67 32.82 +GCC 4 31.53 17.94 18.41 32.11 +GCC 5 32.47 17.01 18.72 31.80 +GCC 6 31.91 19.22 18.59 30.27 +GCC 7 32.05 17.49 19.16 31.31 +GCC 8 31.60 18.48 18.32 31.59 +GCC 9 31.45 18.40 17.96 32.19 +GCC 10 32.14 18.01 18.87 30.98 +GCC 11 32.02 17.56 17.86 32.56 +GCC 12 32.05 17.61 18.00 32.35 +GCC 13 31.86 17.67 18.59 31.88 +GCC 14 31.72 17.68 18.44 32.16 +GCC 15 31.63 18.03 17.98 32.36 +GCC 16 32.03 17.72 18.48 31.77 +GCC 17 31.99 18.40 18.01 31.60 +GCC 18 31.61 18.34 18.24 31.81 +GCC 19 31.84 18.21 17.94 32.01 +GCC 20 32.10 18.22 17.92 31.77 +GCC 21 31.16 18.79 18.17 31.88 +GCC 22 31.98 18.41 18.26 31.35 +GCC 23 31.15 18.33 18.55 31.97 +GCC 24 31.37 18.48 18.52 31.62 +GCC 25 31.47 18.65 18.30 31.58 +GCC 26 31.87 18.40 18.15 31.57 +GCC 27 31.79 18.93 18.30 30.99 +GCC 28 31.17 18.50 18.94 31.40 +GCC 29 30.95 18.34 19.01 31.71 +GCC 30 31.41 18.62 18.06 31.91 +GCC 31 31.69 18.55 18.60 31.16 +GCC 32 30.93 18.48 18.64 31.95 +GCC 33 31.31 18.78 18.14 31.77 +GCC 34 31.30 18.80 18.34 31.56 +GCC 35 31.03 18.43 18.82 31.72 +GCC 36 31.36 18.62 18.87 31.15 +GCC 37 31.27 18.66 18.51 31.56 +GCC 38 31.03 18.62 18.68 31.67 +GCC 39 30.97 18.78 18.84 31.41 +GCC 40 31.73 17.98 18.61 31.69 +GCC 41 31.02 18.70 18.78 31.49 +GCC 42 31.40 18.73 18.70 31.17 +GCC 43 31.56 18.47 19.10 30.88 +GCC 44 30.82 18.22 19.46 31.51 +GCC 45 31.24 18.89 18.40 31.48 +GCC 46 31.46 19.30 18.58 30.66 +GCC 47 31.54 18.24 18.77 31.45 +GCC 48 31.79 18.02 18.46 31.73 +GCC 49 31.56 18.52 18.26 31.66 +GCC 50 31.36 18.36 18.74 31.54 +GCC 51 30.58 18.59 18.76 32.07 +GCC 52 31.06 18.64 18.79 31.50 +GCC 53 31.61 18.60 18.17 31.62 +GCC 54 30.99 18.94 18.45 31.62 +GCC 55 31.18 18.83 19.04 30.94 +GCC 56 32.06 18.78 18.29 30.87 +GCC 57 31.92 18.31 18.75 31.02 +GCC 58 31.02 18.81 18.38 31.79 +GCC 59 31.61 18.11 18.41 31.87 +GCC 60 31.44 18.79 18.67 31.10 +GCC 61 31.69 18.24 18.63 31.44 +GCC 62 31.42 18.27 18.80 31.51 +GCC 63 31.65 18.55 18.45 31.35 +GCC 64 31.01 18.92 18.45 31.62 +GCC 65 31.64 18.14 18.19 32.03 +GCC 66 31.36 18.73 18.23 31.68 +GCC 67 31.38 18.32 18.30 32.00 +GCC 68 31.42 18.17 18.58 31.83 +GCC 69 30.92 19.26 18.48 31.34 +GCC 70 31.47 18.60 18.31 31.62 +GCC 71 31.47 18.52 18.42 31.59 +GCC 72 31.45 18.84 18.74 30.96 +GCC 73 31.62 18.20 18.52 31.65 +GCC 74 31.49 18.05 18.87 31.59 +GCC 75 31.44 18.36 18.46 31.75 +GCC 76 31.71 18.40 18.42 31.46 +GCC 77 31.86 17.97 18.43 31.74 +GCC 78 31.26 18.82 18.45 31.47 +GCC 79 31.50 18.77 17.94 31.80 +GCC 80 31.23 18.60 18.48 31.68 +GCC 81 31.67 18.49 18.37 31.47 +GCC 82 31.49 18.40 18.47 31.64 +GCC 83 31.50 18.67 18.08 31.75 +GCC 84 31.56 17.94 18.46 32.03 +GCC 85 31.56 18.77 18.20 31.46 +GCC 86 31.68 18.16 18.38 31.78 +GCC 87 30.95 18.35 19.10 31.60 +GCC 88 31.91 18.88 18.31 30.90 +GCC 89 31.82 18.46 18.53 31.20 +GCC 90 31.64 18.60 18.54 31.22 +GCC 91 31.76 18.66 18.17 31.41 +GCC 92 32.12 18.25 18.42 31.22 +GCC 93 31.22 18.20 18.60 31.98 +GCC 94 31.07 18.63 18.61 31.69 +GCC 95 31.47 18.22 18.26 32.05 +GCC 96 31.35 18.71 18.66 31.28 +GCC 97 31.63 18.36 18.10 31.92 +GCC 98 31.83 18.22 18.42 31.53 +GCC 99 31.60 18.12 18.44 31.84 +GCC 100 31.04 18.96 18.50 31.49 +GCC 101 31.74 18.57 18.75 30.94 # Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs # Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count -RL 101 25000 -# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count -# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count +RL 101 25001 # Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions ID 1 17 10 ID 2 8 1 @@ -382,17 +474,17 @@ IC 85 0 0 0 1 IC 88 0 3 0 0 IC 92 0 0 0 1 # Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. -COV [1-1] 1 30808 -COV [2-2] 2 5369 -COV [3-3] 3 1121 -COV [4-4] 4 384 -COV [5-5] 5 65 -COV [6-6] 6 45 +COV [1-1] 1 31856 +COV [2-2] 2 5793 +COV [3-3] 3 1266 +COV [4-4] 4 489 +COV [5-5] 5 160 +COV [6-6] 6 49 COV [7-7] 7 36 # GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile GCD 0.0 15.385 0.000 0.000 0.000 0.000 0.000 -GCD 6.6 23.077 0.086 0.086 0.086 0.086 0.086 -GCD 38.0 30.769 0.141 0.141 0.141 0.141 0.141 -GCD 40.0 61.538 0.141 0.141 0.202 0.212 0.288 -GCD 41.0 92.308 0.172 0.172 0.197 0.222 0.258 -GCD 42.0 100.000 0.152 0.152 0.152 0.152 0.152 +GCD 6.6 23.077 0.085 0.085 0.085 0.085 0.085 +GCD 38.0 30.769 0.140 0.140 0.140 0.140 0.140 +GCD 40.0 69.231 0.140 0.140 0.200 0.210 0.285 +GCD 41.0 92.308 0.195 0.195 0.220 0.255 0.255 +GCD 42.0 100.000 0.150 0.150 0.150 0.150 0.150 diff --git a/results/bwa/C.sorted.bam b/results/bwa/C.sorted.bam index a72927b1b0d81449f26001365e7745ccece56900..ed237ddee327d304e2a5271a42daa5bd10328d4f 100644 GIT binary patch delta 137 zcmWN=$qfMk06@_UW5#am`x-79aF@`CvmzY6#Ld5`KnpGka8-mv853UeQZ7OIe_aM& zSDSeM+?}J>&BHoOKJWWU3^0RP3^9ih#+b(f7O{k7tY8&um|z_n*u)mLv4dUgVIK!L R#1W2hf>WH~{Ndub{Q>jvHje-R delta 137 zcmWN=Ne;mP06@`{QuC~4O4zu7h1f`3z!k*OAuN6qJO3~?t|M`bhL^mIN09wL*TKil zF8aPtX&T2~w&CHtzuv_FbC|~v3s}SmOIXGVR - + - [insane_legentil] Nextflow Workflow Report + [jolly_lichterman] Nextflow Workflow Report