BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472544.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,476,916 number of mapped reads = 15,249,447 (98.53%) number of supplementary alignments = 65,669 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,642,713 number of mapped paired reads (second in pair) = 7,606,734 number of mapped paired reads (both in pair) = 15,151,774 number of mapped paired reads (singletons) = 97,673 number of mapped bases = 1,497,037,056 bp number of sequenced bases = 1,496,866,542 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,912,847 duplication rate = 42.88% >>>>>>> Insert size mean insert size = 37,503.7143 std insert size = 1,900,692.916 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 54.8889 >>>>>>> ACTG content number of A's = 410,676,636 bp (27.44%) number of C's = 340,195,904 bp (22.73%) number of T's = 407,599,700 bp (27.23%) number of G's = 338,160,868 bp (22.59%) number of N's = 233,434 bp (0.02%) GC percentage = 45.32% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 8,453,024 number of insertions = 68,724 mapped reads with insertion percentage = 0.45% number of deletions = 72,074 mapped reads with deletion percentage = 0.47% homopolymer indels = 42.93% >>>>>>> Coverage mean coverageData = 0.4836X std coverageData = 26.2179X There is a 4.98% of reference with a coverageData >= 1X There is a 2.32% of reference with a coverageData >= 2X There is a 1.02% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.34% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.27% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.25% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.22% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.21% of reference with a coverageData >= 17X There is a 0.2% of reference with a coverageData >= 18X There is a 0.2% of reference with a coverageData >= 19X There is a 0.19% of reference with a coverageData >= 20X There is a 0.19% of reference with a coverageData >= 21X There is a 0.18% of reference with a coverageData >= 22X There is a 0.18% of reference with a coverageData >= 23X There is a 0.18% of reference with a coverageData >= 24X There is a 0.17% of reference with a coverageData >= 25X There is a 0.17% of reference with a coverageData >= 26X There is a 0.16% of reference with a coverageData >= 27X There is a 0.16% of reference with a coverageData >= 28X There is a 0.16% of reference with a coverageData >= 29X There is a 0.16% of reference with a coverageData >= 30X There is a 0.15% of reference with a coverageData >= 31X There is a 0.15% of reference with a coverageData >= 32X There is a 0.15% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.14% of reference with a coverageData >= 35X There is a 0.14% of reference with a coverageData >= 36X There is a 0.14% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.13% of reference with a coverageData >= 39X There is a 0.13% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.12% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 167783847 0.6731531754137535 33.83863966685176 chr2 243199373 104802811 0.43093372202073893 20.51345770541588 chr3 198022430 152240811 0.7688058923425998 22.523406772768944 chr4 191154276 66192348 0.34627709819057356 21.887289905044 chr5 180915260 74904507 0.41403089490626716 20.111097464736513 chr6 171115067 105281899 0.6152696010106462 23.3569102310342 chr7 159138663 51396317 0.3229656202402555 12.011323965789 chr8 146364022 83325154 0.5693007944261056 22.02509807969731 chr9 141213431 130993857 0.9276302974325438 46.760279578730504 chr10 135534747 34255727 0.2527449805915822 11.054666835667257 chr11 135006516 57726286 0.42758148058572226 17.188364367326034 chr12 133851895 72888954 0.5445492871057224 17.282939648307554 chr13 115169878 38917097 0.3379103779201711 20.129878338751503 chr14 107349540 31688922 0.2951938312916851 16.755409434941427 chr15 102531392 25337615 0.24712055991593287 9.2591980772325 chr16 90354753 48605246 0.5379378990721163 21.526011568291196 chr17 81195210 49841718 0.6138504722138165 20.22718153059748 chr18 78077248 34360121 0.44007853606725483 26.554283448134726 chr19 59128983 21048632 0.3559782518160341 11.612474213541526 chr20 63025520 19252075 0.3054647545946467 9.104879002816185 chr21 48129895 7495485 0.15573449723918992 6.163167355785415 chr22 51304566 10524171 0.2051312742807336 7.5086575396625586 chrMT 16571 7524 0.4540462253334138 1.6453707661481496 chrX 155270560 104345399 0.6720230737881026 64.58088308182222 chrY 59373566 3820533 0.0643473730380284 4.311876630155508