BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716219.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 = 866,127 number of mapped reads = 750,914 (86.7%) number of supplementary alignments = 4,721 (0.55%) number of secondary alignments = 0 number of mapped bases = 44,018,902 bp number of sequenced bases = 44,005,623 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,384 duplication rate = 2.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2105 >>>>>>> ACTG content number of A's = 11,747,711 bp (26.7%) number of C's = 8,197,798 bp (18.63%) number of T's = 13,431,693 bp (30.52%) number of G's = 10,627,975 bp (24.15%) number of N's = 446 bp (0%) GC percentage = 42.78% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 221,470 number of insertions = 3,794 mapped reads with insertion percentage = 0.5% number of deletions = 8,150 mapped reads with deletion percentage = 1.08% homopolymer indels = 40.2% >>>>>>> Coverage mean coverageData = 0.0142X std coverageData = 0.1544X There is a 1.3% 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 3496849 0.01402944949934548 0.20759649571003644 chr2 243199373 3734052 0.015353871821042893 0.1956962820283046 chr3 198022430 2923707 0.01476452440261439 0.129429714277936 chr4 191154276 2823797 0.014772345453574892 0.1464624491900673 chr5 180915260 2619470 0.014478988671270737 0.12872011571478276 chr6 171115067 2491758 0.014561885424151457 0.1330190398078916 chr7 159138663 2407286 0.015126971375900022 0.1804115703874585 chr8 146364022 2215934 0.015139881848833041 0.1699870117531688 chr9 141213431 1843429 0.013054204454532373 0.1321177641780904 chr10 135534747 2121914 0.015655867199870156 0.17809837035796558 chr11 135006516 2019560 0.014958981683521113 0.14601851837365712 chr12 133851895 1992931 0.01488907572059402 0.1310762104756547 chr13 115169878 1353939 0.011756016620943196 0.11568661440557775 chr14 107349540 1341912 0.012500398231794939 0.11971006380312359 chr15 102531392 1302304 0.012701514868734056 0.12117735250405133 chr16 90354753 1294837 0.014330590887675826 0.13180284857679725 chr17 81195210 1232518 0.01517968855551947 0.13641128596355992 chr18 78077248 1158864 0.014842531335120828 0.20621410427136824 chr19 59128983 914419 0.015464818666000055 0.17160665772438743 chr20 63025520 949390 0.015063580594019693 0.13307043297776602 chr21 48129895 604242 0.01255440096015169 0.13341821510315627 chr22 51304566 552560 0.010770191487439929 0.11066599723582951 chrMT 16571 14997 0.9050147848651259 1.1213096372966354 chrX 155270560 2457871 0.01582960092370376 0.13869262369056468 chrY 59373566 150362 0.002532473794819735 0.09738539568910673