BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524473.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 584,386 number of mapped reads = 539,569 (92.33%) number of supplementary alignments = 1,209 (0.21%) number of secondary alignments = 0 number of mapped bases = 31,433,628 bp number of sequenced bases = 31,423,778 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,237 duplication rate = 1.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4635 >>>>>>> ACTG content number of A's = 8,071,989 bp (25.69%) number of C's = 5,570,006 bp (17.73%) number of T's = 9,810,579 bp (31.22%) number of G's = 7,970,561 bp (25.36%) number of N's = 643 bp (0%) GC percentage = 43.09% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 143,683 number of insertions = 1,660 mapped reads with insertion percentage = 0.31% number of deletions = 5,775 mapped reads with deletion percentage = 1.07% homopolymer indels = 44.92% >>>>>>> Coverage mean coverageData = 0.0102X std coverageData = 0.1232X There is a 0.96% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3112413 0.012487082228774066 0.18018768892456366 chr2 243199373 2479313 0.010194569868401757 0.1333848235071931 chr3 198022430 1730418 0.008738494927064576 0.09780089938302444 chr4 191154276 1779105 0.009307168205852742 0.10396691895167345 chr5 180915260 1715293 0.009481195781936803 0.10140414548902271 chr6 171115067 1363802 0.007970087169471757 0.1024761115965778 chr7 159138663 1581199 0.009935982684484411 0.14773593069524502 chr8 146364022 2872086 0.019622896124021516 0.15497174365155297 chr9 141213431 1262985 0.008943802236488397 0.11100353253695798 chr10 135534747 1646057 0.01214490775564734 0.12891201067645958 chr11 135006516 1085223 0.008038300906898449 0.11275906242061787 chr12 133851895 1446652 0.01080785595153509 0.10845729708898393 chr13 115169878 709684 0.006162062618491269 0.08229947741926352 chr14 107349540 757749 0.007058707470940257 0.0881538405577081 chr15 102531392 853085 0.008320232305048584 0.09569105574769231 chr16 90354753 998548 0.011051416409715601 0.1125040302228711 chr17 81195210 1095144 0.013487790720659507 0.12278416741508377 chr18 78077248 759727 0.009730453102035564 0.1721318779235181 chr19 59128983 603342 0.010203828467673797 0.14298167756078625 chr20 63025520 876668 0.013909730534551717 0.12303249465390662 chr21 48129895 435706 0.009052710378861205 0.10183392398114019 chr22 51304566 261038 0.00508800717659321 0.07435265305913863 chrMT 16571 28560 1.7234928489529902 1.6758914881160276 chrX 155270560 1884077 0.012134154729653839 0.11966789847088562 chrY 59373566 95754 0.0016127378975350748 0.05372959789514238