BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716465.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 = 626,460 number of mapped reads = 573,670 (91.57%) number of supplementary alignments = 1,904 (0.3%) number of secondary alignments = 0 number of mapped bases = 33,076,254 bp number of sequenced bases = 33,065,906 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,352 duplication rate = 1.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8394 >>>>>>> ACTG content number of A's = 7,839,398 bp (23.71%) number of C's = 5,805,005 bp (17.56%) number of T's = 11,032,595 bp (33.37%) number of G's = 8,388,189 bp (25.37%) number of N's = 719 bp (0%) GC percentage = 42.92% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 169,476 number of insertions = 2,016 mapped reads with insertion percentage = 0.35% number of deletions = 6,312 mapped reads with deletion percentage = 1.09% homopolymer indels = 45.43% >>>>>>> Coverage mean coverageData = 0.0107X std coverageData = 0.1327X There is a 1.02% of reference with a coverageData >= 1X There is a 0.03% 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 2768807 0.01110852598437458 0.19083685060492434 chr2 243199373 2619999 0.010773049978216844 0.16693689463026185 chr3 198022430 1916098 0.009676166482756524 0.10228548925532498 chr4 191154276 2063832 0.01079668236142413 0.11346757340884572 chr5 180915260 1912443 0.01057093249071416 0.10645348887803704 chr6 171115067 1778641 0.010394414888082298 0.11577205954626921 chr7 159138663 1906369 0.011979295062947714 0.1603268955647216 chr8 146364022 1738349 0.011876887340524162 0.1662523208226962 chr9 141213431 1083974 0.007676139530948724 0.10033569750794108 chr10 135534747 1469168 0.010839788559903387 0.14288102750691187 chr11 135006516 1158754 0.008582948692639399 0.10671804312179982 chr12 133851895 1643111 0.012275590121454762 0.11466974484252125 chr13 115169878 1010874 0.008777242952362943 0.09696832918922169 chr14 107349540 1127194 0.010500221985115167 0.10677465465942407 chr15 102531392 1203739 0.011740199528355179 0.11185802038811803 chr16 90354753 1112106 0.012308218030323208 0.11740111393618825 chr17 81195210 1399718 0.017238923330575782 0.13757552983060375 chr18 78077248 635192 0.00813543018319498 0.1417416729222412 chr19 59128983 835672 0.014133035232484888 0.16596627712904863 chr20 63025520 1045589 0.016589930555114818 0.13472128896974325 chr21 48129895 410664 0.00853241005408385 0.10304958116711065 chr22 51304566 299910 0.005845678530834858 0.0785566769260406 chrMT 16571 28252 1.7049061613662422 1.6346195975630446 chrX 155270560 1791772 0.011539676291500461 0.11574734045842103 chrY 59373566 116027 0.0019541861440493568 0.08757038303582829