BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960917.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 229,224,264 number of mapped reads = 224,561,281 (97.97%) number of supplementary alignments = 470,210 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 112,747,381 number of mapped paired reads (second in pair) = 111,813,900 number of mapped paired reads (both in pair) = 222,649,058 number of mapped paired reads (singletons) = 1,912,223 number of mapped bases = 21,950,396,484 bp number of sequenced bases = 21,944,045,855 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,322,175 duplication rate = 12.29% >>>>>>> Insert size mean insert size = 18,877.7346 std insert size = 1,275,135.0051 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 53.5808 >>>>>>> ACTG content number of A's = 6,721,112,165 bp (30.63%) number of C's = 4,260,876,133 bp (19.42%) number of T's = 6,715,789,935 bp (30.6%) number of G's = 4,243,376,615 bp (19.34%) number of N's = 2,891,007 bp (0.01%) GC percentage = 38.75% >>>>>>> Mismatches and indels general error rate = 0.0143 number of mismatches = 307,934,009 number of insertions = 2,628,299 mapped reads with insertion percentage = 1.14% number of deletions = 2,918,703 mapped reads with deletion percentage = 1.26% homopolymer indels = 40.48% >>>>>>> Coverage mean coverageData = 7.0906X std coverageData = 105.3469X There is a 89.51% of reference with a coverageData >= 1X There is a 85.39% of reference with a coverageData >= 2X There is a 79.32% of reference with a coverageData >= 3X There is a 71.74% of reference with a coverageData >= 4X There is a 63.23% of reference with a coverageData >= 5X There is a 54.41% of reference with a coverageData >= 6X There is a 45.8% of reference with a coverageData >= 7X There is a 37.81% of reference with a coverageData >= 8X There is a 30.67% of reference with a coverageData >= 9X There is a 24.5% of reference with a coverageData >= 10X There is a 19.31% of reference with a coverageData >= 11X There is a 15.06% of reference with a coverageData >= 12X There is a 11.64% of reference with a coverageData >= 13X There is a 8.94% of reference with a coverageData >= 14X There is a 6.84% of reference with a coverageData >= 15X There is a 5.22% of reference with a coverageData >= 16X There is a 3.98% of reference with a coverageData >= 17X There is a 3.04% of reference with a coverageData >= 18X There is a 2.33% of reference with a coverageData >= 19X There is a 1.8% of reference with a coverageData >= 20X There is a 1.4% of reference with a coverageData >= 21X There is a 1.1% of reference with a coverageData >= 22X There is a 0.88% of reference with a coverageData >= 23X There is a 0.72% of reference with a coverageData >= 24X There is a 0.6% of reference with a coverageData >= 25X There is a 0.5% of reference with a coverageData >= 26X There is a 0.44% of reference with a coverageData >= 27X There is a 0.39% of reference with a coverageData >= 28X There is a 0.35% of reference with a coverageData >= 29X There is a 0.32% of reference with a coverageData >= 30X There is a 0.29% of reference with a coverageData >= 31X There is a 0.28% of reference with a coverageData >= 32X There is a 0.26% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1824210475 7.318780060331324 279.350868239218 chr2 243199373 1848059175 7.598947119818438 56.17798472142019 chr3 198022430 1632769263 8.245375349651047 9.668748836072504 chr4 191154276 1449627191 7.583545716759169 57.3870962328331 chr5 180915260 1193500588 6.597014469647282 9.46070168268281 chr6 171115067 1154032122 6.744187652394164 27.687223143256418 chr7 159138663 1207073849 7.585044553252279 69.17353351902662 chr8 146364022 1287710993 8.798002237189136 134.72794607439602 chr9 141213431 936418064 6.631225212564944 99.6617211501792 chr10 135534747 1045827938 7.7163086304355595 201.69457396133683 chr11 135006516 1069553640 7.922237175574548 43.97319415119848 chr12 133851895 992096542 7.411897620127082 11.891521518282913 chr13 115169878 757528327 6.577486580301839 4.900695036855989 chr14 107349540 467187418 4.352020679362017 7.390994430241028 chr15 102531392 590677577 5.760943702002993 5.202512245720827 chr16 90354753 720798711 7.977429931107221 86.20731463137746 chr17 81195210 418394653 5.152947482985757 26.329502447862236 chr18 78077248 843216485 10.799772105184855 102.41257799751699 chr19 59128983 405307462 6.85463272723632 116.82211129348573 chr20 63025520 412276309 6.541418603130922 19.116319433206527 chr21 48129895 292119462 6.069397450378814 23.120749184771945 chr22 51304566 225812593 4.401413180261578 5.754446105791194 chrMT 16571 5006547 302.1270291473055 62.1848043988856 chrX 155270560 1110965471 7.155029717159518 29.61202173807784 chrY 59373566 60225629 1.0143508813332855 53.26588604153256