BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716842.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 = 601,681 number of mapped reads = 542,998 (90.25%) number of supplementary alignments = 8,192 (1.36%) number of secondary alignments = 0 number of mapped bases = 43,173,177 bp number of sequenced bases = 43,154,272 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,517 duplication rate = 1.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8186 >>>>>>> ACTG content number of A's = 11,000,669 bp (25.49%) number of C's = 8,308,822 bp (19.25%) number of T's = 13,007,714 bp (30.14%) number of G's = 10,834,907 bp (25.11%) number of N's = 2,160 bp (0.01%) GC percentage = 44.36% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 357,705 number of insertions = 4,345 mapped reads with insertion percentage = 0.78% number of deletions = 11,004 mapped reads with deletion percentage = 1.99% homopolymer indels = 43.03% >>>>>>> Coverage mean coverageData = 0.0139X std coverageData = 0.1881X There is a 1.29% of reference with a coverageData >= 1X There is a 0.06% 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 3443547 0.013815600483498896 0.2611121376289764 chr2 243199373 3788828 0.015579102664874058 0.2603775486340995 chr3 198022430 2855418 0.014419669529355842 0.12600556693697673 chr4 191154276 2683176 0.014036704049455844 0.13122617979702889 chr5 180915260 2532865 0.014000283889816702 0.12550032084927445 chr6 171115067 2483289 0.01451239241252788 0.1368599370132827 chr7 159138663 2356101 0.014805333635359246 0.21596275248128682 chr8 146364022 2176695 0.014871790008612908 0.2447389619901605 chr9 141213431 1787042 0.01265490107665467 0.21080133371312815 chr10 135534747 2090627 0.01542502602672066 0.19162320642455782 chr11 135006516 1928931 0.014287688158695985 0.18310589645609554 chr12 133851895 1995325 0.014906961160318276 0.12900647348725522 chr13 115169878 1320586 0.011466418328584147 0.11157514973186479 chr14 107349540 1268888 0.011820153118494965 0.13980929732484185 chr15 102531392 1236217 0.012056961052474544 0.11605673152786614 chr16 90354753 1280099 0.014167478273113092 0.13724640114927827 chr17 81195210 1214102 0.014952877146324272 0.13846275367456443 chr18 78077248 1232170 0.015781422009136386 0.37837616610401875 chr19 59128983 950850 0.01608094629329241 0.235596548434728 chr20 63025520 870658 0.013814372336793095 0.12637095956426792 chr21 48129895 547757 0.011380806045805835 0.11761022013303794 chr22 51304566 491425 0.009578582148029476 0.10211988505554752 chrMT 16571 7048 0.4253213445175306 0.721665118674531 chrX 155270560 2514837 0.01619648309376871 0.16381890547018918 chrY 59373566 116696 0.00196545378460172 0.07006151398314993