BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525152.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 = 1,279,128 number of mapped reads = 1,217,320 (95.17%) number of supplementary alignments = 5,780 (0.45%) number of secondary alignments = 0 number of mapped bases = 77,922,073 bp number of sequenced bases = 77,896,224 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,893 duplication rate = 1.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3838 >>>>>>> ACTG content number of A's = 20,806,335 bp (26.71%) number of C's = 17,395,871 bp (22.33%) number of T's = 22,709,461 bp (29.15%) number of G's = 16,982,449 bp (21.8%) number of N's = 2,108 bp (0%) GC percentage = 44.13% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 360,703 number of insertions = 4,885 mapped reads with insertion percentage = 0.4% number of deletions = 15,701 mapped reads with deletion percentage = 1.28% homopolymer indels = 44.86% >>>>>>> Coverage mean coverageData = 0.0252X std coverageData = 0.2539X There is a 2.31% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% 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 8582682 0.0344339442989793 0.5169355759770562 chr2 243199373 6666192 0.027410399614804928 0.23728273899541572 chr3 198022430 6199084 0.03130495873624013 0.18979143279975838 chr4 191154276 4339437 0.02270122903240731 0.16841529307688055 chr5 180915260 3532258 0.01952437842998982 0.14838220092294624 chr6 171115067 3928083 0.02295579850954913 0.18002833933552861 chr7 159138663 4671723 0.02935630419365783 0.3832856154013623 chr8 146364022 3679716 0.02514085052951059 0.20202867333639787 chr9 141213431 2619569 0.0185504238615943 0.1949008960512745 chr10 135534747 4332018 0.031962416250350914 0.28121388854997553 chr11 135006516 3752388 0.027794125136893392 0.20709132936137437 chr12 133851895 3655839 0.027312568118665784 0.1772717643191385 chr13 115169878 2418090 0.02099585448896629 0.15285071786522 chr14 107349540 3002512 0.027969491066286822 0.1835702244631641 chr15 102531392 2224534 0.02169612600207359 0.15571718193189862 chr16 90354753 2173181 0.024051651162169632 0.18034772794347353 chr17 81195210 1600175 0.019707751233108455 0.15622477519049527 chr18 78077248 1700652 0.021781659107657073 0.3719994326781705 chr19 59128983 1481903 0.025062210185485517 0.35197275197209876 chr20 63025520 1502013 0.023831822410985266 0.16701769433106914 chr21 48129895 1026999 0.02133806857463537 0.16200790177355145 chr22 51304566 676082 0.013177813452315336 0.12075844704352443 chrMT 16571 23896 1.44203729406795 1.3872574820210046 chrX 155270560 3910544 0.025185353875196947 0.17753243176172948 chrY 59373566 222503 0.003747509455638895 0.13027119651489072