BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716739.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 = 874,990 number of mapped reads = 808,768 (92.43%) number of supplementary alignments = 4,338 (0.5%) number of secondary alignments = 0 number of mapped bases = 47,349,237 bp number of sequenced bases = 47,335,589 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,927 duplication rate = 1.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6482 >>>>>>> ACTG content number of A's = 11,759,165 bp (24.84%) number of C's = 9,515,804 bp (20.1%) number of T's = 14,565,416 bp (30.77%) number of G's = 11,494,567 bp (24.28%) number of N's = 637 bp (0%) GC percentage = 44.39% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 232,863 number of insertions = 3,168 mapped reads with insertion percentage = 0.39% number of deletions = 8,629 mapped reads with deletion percentage = 1.06% homopolymer indels = 41.37% >>>>>>> Coverage mean coverageData = 0.0153X std coverageData = 0.1725X There is a 1.42% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% 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 3675928 0.014747919123539515 0.22357695013225617 chr2 243199373 4503370 0.01851719412122004 0.19043464390206521 chr3 198022430 3807751 0.019228887353821483 0.15011469008465486 chr4 191154276 3359997 0.01757740956838444 0.14627005068786839 chr5 180915260 2162603 0.011953679308202084 0.11418093672227783 chr6 171115067 2336819 0.013656418695146232 0.12946794056091593 chr7 159138663 2841710 0.01785681710798337 0.3401966241614137 chr8 146364022 3684012 0.025170202004970867 0.20679661142321645 chr9 141213431 1927380 0.013648701730078353 0.1337903763867378 chr10 135534747 2217703 0.016362615853778073 0.22133413658577528 chr11 135006516 1624443 0.012032330350632853 0.13034236942158195 chr12 133851895 2151621 0.01607463980991827 0.14263558368699583 chr13 115169878 1161684 0.010086699926868031 0.10572533695013196 chr14 107349540 1139804 0.010617688720417432 0.10956693628436943 chr15 102531392 1055608 0.010295461510948763 0.10645283085730861 chr16 90354753 1441961 0.01595888375678477 0.1367500101241528 chr17 81195210 2045296 0.025189860337820422 0.16937659556483448 chr18 78077248 1093437 0.014004553541641223 0.17829696686765678 chr19 59128983 999434 0.01690260764336163 0.2163017273479797 chr20 63025520 1048014 0.01662840703257982 0.13813458979895024 chr21 48129895 475714 0.009883960893743899 0.10977486923643412 chr22 51304566 837771 0.016329365304444832 0.13441094555861174 chrMT 16571 30184 1.8214953835012975 1.6985631367669736 chrX 155270560 1615378 0.010403633502706502 0.11466143559333139 chrY 59373566 111615 0.001879876980944685 0.06348796842837208