BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524806.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 = 1,489,162 number of mapped reads = 1,330,997 (89.38%) number of supplementary alignments = 4,675 (0.31%) number of secondary alignments = 0 number of mapped bases = 75,075,164 bp number of sequenced bases = 75,051,668 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,296 duplication rate = 2.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3154 >>>>>>> ACTG content number of A's = 19,161,874 bp (25.53%) number of C's = 12,935,004 bp (17.23%) number of T's = 23,976,022 bp (31.95%) number of G's = 18,969,968 bp (25.28%) number of N's = 8,800 bp (0.01%) GC percentage = 42.51% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 388,867 number of insertions = 5,829 mapped reads with insertion percentage = 0.44% number of deletions = 14,486 mapped reads with deletion percentage = 1.08% homopolymer indels = 41.98% >>>>>>> Coverage mean coverageData = 0.0243X std coverageData = 0.2243X There is a 2.18% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5932327 0.023800650831678368 0.27810093084647985 chr2 243199373 6349744 0.02610921204965442 0.37391418874371035 chr3 198022430 4968352 0.025089844620127123 0.17481209004927595 chr4 191154276 4866369 0.025457808749201092 0.1971365285840663 chr5 180915260 4482641 0.02477757266026094 0.1717292858909582 chr6 171115067 4264349 0.024920943986773532 0.18906249959441782 chr7 159138663 4082275 0.025652314296495 0.2597508547197219 chr8 146364022 3698952 0.025272276270188857 0.211167860281248 chr9 141213431 3198816 0.022652349548818767 0.1958564109564269 chr10 135534747 3654292 0.02696203062968052 0.2614656898908996 chr11 135006516 3386238 0.025082033818278816 0.20817666904095156 chr12 133851895 3370688 0.025182220991342708 0.17460796258387604 chr13 115169878 2368512 0.020565377346323143 0.1563677512289337 chr14 107349540 2295560 0.0213839761213695 0.16257503732540754 chr15 102531392 2150953 0.02097848237542703 0.15993284007328457 chr16 90354753 2263432 0.025050502877253175 0.1894322995609872 chr17 81195210 2094995 0.02580195309550896 0.18271601971738144 chr18 78077248 1970903 0.025242987560217287 0.2877486500688913 chr19 59128983 1610400 0.02723537457087669 0.2429602222347633 chr20 63025520 1628740 0.025842547590245984 0.18417823042428988 chr21 48129895 996385 0.0207019982071434 0.17271913244530854 chr22 51304566 928035 0.018088740873473133 0.14690213302919017 chrMT 16571 27871 1.681914187435882 1.5524048586879147 chrX 155270560 4229718 0.027240952824540594 0.1913881048448404 chrY 59373566 254617 0.004288389887176391 0.12459621416332761