BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716456.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 = 1,052,338 number of mapped reads = 877,609 (83.4%) number of supplementary alignments = 5,017 (0.48%) number of secondary alignments = 0 number of mapped bases = 49,567,987 bp number of sequenced bases = 49,553,943 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,802 duplication rate = 1.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.2193 >>>>>>> ACTG content number of A's = 11,986,051 bp (24.19%) number of C's = 9,868,692 bp (19.92%) number of T's = 15,382,062 bp (31.04%) number of G's = 12,316,768 bp (24.86%) number of N's = 370 bp (0%) GC percentage = 44.77% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 258,867 number of insertions = 3,824 mapped reads with insertion percentage = 0.43% number of deletions = 8,170 mapped reads with deletion percentage = 0.92% homopolymer indels = 37.53% >>>>>>> Coverage mean coverageData = 0.016X std coverageData = 0.1754X There is a 1.51% of reference with a coverageData >= 1X There is a 0.05% 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 4014167 0.016104942823793406 0.2549905331272524 chr2 243199373 4083337 0.016790080293504706 0.24539734397372145 chr3 198022430 3200478 0.016162199403370617 0.13261809426582194 chr4 191154276 3080255 0.01611397382499568 0.1486436636014724 chr5 180915260 2864180 0.015831610887881983 0.13093057752527648 chr6 171115067 2767985 0.01617616174033348 0.14680271152849866 chr7 159138663 2757762 0.017329302307887304 0.21401987689328766 chr8 146364022 2433891 0.016629025130233167 0.1718231727176302 chr9 141213431 2059014 0.01458086518696653 0.1484274338505014 chr10 135534747 2437558 0.01798474600760497 0.21452426500038504 chr11 135006516 2217382 0.01642425910761226 0.1562245889875527 chr12 133851895 2288201 0.017095021329358095 0.13834031972442695 chr13 115169878 1471376 0.012775701646571163 0.11805009408271268 chr14 107349540 1506225 0.014031033574992496 0.13035848952565532 chr15 102531392 1466802 0.014305882046349278 0.12682254432650222 chr16 90354753 1555239 0.017212586481200387 0.1479796772059244 chr17 81195210 1536881 0.018928222489972005 0.14887504407531596 chr18 78077248 1254062 0.016061810990059485 0.22722604826094608 chr19 59128983 1250810 0.02115392378725675 0.2230067993202076 chr20 63025520 1106747 0.017560299383487833 0.14104698469141166 chr21 48129895 637079 0.013236658837506294 0.13490054779257496 chr22 51304566 641874 0.012511050186059462 0.11690196711842747 chrMT 16571 13867 0.8368233661215376 1.018193203472298 chrX 155270560 2735811 0.017619637618361137 0.14988688218983665 chrY 59373566 187004 0.0031496171208581273 0.11930324472740635