BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716823.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 = 760,685 number of mapped reads = 598,497 (78.68%) number of supplementary alignments = 664 (0.09%) number of secondary alignments = 0 number of mapped bases = 31,372,779 bp number of sequenced bases = 31,365,420 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,251 duplication rate = 5.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9974 >>>>>>> ACTG content number of A's = 6,913,509 bp (22.04%) number of C's = 6,051,547 bp (19.29%) number of T's = 9,941,725 bp (31.7%) number of G's = 8,458,044 bp (26.97%) number of N's = 595 bp (0%) GC percentage = 46.26% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 198,983 number of insertions = 1,940 mapped reads with insertion percentage = 0.32% number of deletions = 4,398 mapped reads with deletion percentage = 0.73% homopolymer indels = 41.51% >>>>>>> Coverage mean coverageData = 0.0101X std coverageData = 0.12X There is a 0.9% of reference with a coverageData >= 1X There is a 0.09% 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 3042764 0.012207648622067024 0.13562752091573488 chr2 243199373 2770840 0.011393285952262714 0.15602817850978215 chr3 198022430 2091294 0.010560894541088097 0.11397141908748529 chr4 191154276 1877146 0.009820057595781953 0.11320326830261092 chr5 180915260 1872544 0.010350392775048385 0.11276332760830161 chr6 171115067 1387455 0.008108315791969389 0.10515029672078491 chr7 159138663 1866818 0.011730763378350112 0.13151936820000623 chr8 146364022 1976380 0.013503181813355743 0.13170579073417285 chr9 141213431 1392615 0.009861774408696294 0.11333486668300014 chr10 135534747 1533671 0.011315703418843583 0.12812940780846171 chr11 135006516 1323429 0.009802704633900781 0.11649846476927557 chr12 133851895 1479721 0.011054912595746216 0.11701237280514849 chr13 115169878 543298 0.0047173619477134466 0.07680829087389449 chr14 107349540 971042 0.009045609324455419 0.10562035608709978 chr15 102531392 614309 0.005991423582740396 0.08567492121447502 chr16 90354753 848582 0.009391669744257947 0.11106245541683296 chr17 81195210 1294596 0.01594424104574642 0.14277426988718497 chr18 78077248 857738 0.010985761178467765 0.12684902938290898 chr19 59128983 860601 0.014554638966139498 0.1552602389856501 chr20 63025520 871735 0.01383146065276415 0.13553320919293205 chr21 48129895 446647 0.00928003271147797 0.11177157093643125 chr22 51304566 364565 0.007105897747970424 0.0959208510638998 chrMT 16571 36633 2.2106692414458995 2.26606149994505 chrX 155270560 964054 0.006208865350907474 0.08889216827051634 chrY 59373566 84302 0.001419857449694027 0.048954005545915356