BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524357.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 = 717,200 number of mapped reads = 634,811 (88.51%) number of supplementary alignments = 8,518 (1.19%) number of secondary alignments = 0 number of mapped bases = 36,365,974 bp number of sequenced bases = 36,356,347 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,884 duplication rate = 1.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.1611 >>>>>>> ACTG content number of A's = 8,667,948 bp (23.84%) number of C's = 6,810,710 bp (18.73%) number of T's = 11,648,671 bp (32.04%) number of G's = 9,223,820 bp (25.37%) number of N's = 5,198 bp (0.01%) GC percentage = 44.1% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 191,160 number of insertions = 2,729 mapped reads with insertion percentage = 0.43% number of deletions = 5,972 mapped reads with deletion percentage = 0.93% homopolymer indels = 40% >>>>>>> Coverage mean coverageData = 0.0117X std coverageData = 0.1663X There is a 1.12% of reference with a coverageData >= 1X There is a 0.03% 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 2946476 0.01182133865175004 0.31801572822106716 chr2 243199373 3006258 0.01236129009263523 0.18181273559967867 chr3 198022430 2382621 0.012032076366298505 0.11308144230459767 chr4 191154276 2273177 0.011891844888680387 0.12043790269928978 chr5 180915260 2157017 0.011922802974165916 0.11347977340220558 chr6 171115067 2059758 0.012037268465669361 0.11979216354945636 chr7 159138663 2075281 0.013040709032474403 0.23617680871060995 chr8 146364022 1984180 0.013556473598409315 0.15532281187303904 chr9 141213431 1530203 0.01083610099382119 0.13886526668689753 chr10 135534747 1747502 0.012893387405666534 0.15159291609671754 chr11 135006516 1659006 0.012288340216112236 0.14612472519335715 chr12 133851895 1638464 0.012240872645097777 0.11685586852114076 chr13 115169878 1095704 0.009513807073755865 0.09969247114291058 chr14 107349540 1088305 0.010137956809130249 0.11459601496430202 chr15 102531392 1051542 0.010255805363492968 0.10493308701040434 chr16 90354753 1075119 0.011898864910847578 0.1214169596160831 chr17 81195210 1021200 0.012577096604590344 0.12183945091932204 chr18 78077248 968116 0.012399463669621143 0.2699386763588454 chr19 59128983 776475 0.013131884916742099 0.20651466080213668 chr20 63025520 767627 0.012179621842072863 0.11631470272649931 chr21 48129895 470072 0.009766736453507742 0.10655951755817906 chr22 51304566 420989 0.008205682901595932 0.09274138627157029 chrMT 16571 11321 0.6831814615895239 0.929961427354727 chrX 155270560 2033129 0.013094104896639775 0.13364462461809917 chrY 59373566 126432 0.002129432481788276 0.06982166306593873