BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525135.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 = 1,618,614 number of mapped reads = 1,446,435 (89.36%) number of supplementary alignments = 35,865 (2.22%) number of secondary alignments = 0 number of mapped bases = 110,962,916 bp number of sequenced bases = 110,920,611 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,789 duplication rate = 1.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3654 >>>>>>> ACTG content number of A's = 29,651,241 bp (26.73%) number of C's = 21,185,293 bp (19.1%) number of T's = 34,701,487 bp (31.28%) number of G's = 25,378,219 bp (22.88%) number of N's = 4,371 bp (0%) GC percentage = 41.98% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 819,938 number of insertions = 9,529 mapped reads with insertion percentage = 0.65% number of deletions = 24,803 mapped reads with deletion percentage = 1.69% homopolymer indels = 42.61% >>>>>>> Coverage mean coverageData = 0.0358X std coverageData = 0.3526X There is a 3.18% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8968748 0.03598285117211403 0.4882044076581462 chr2 243199373 9567056 0.039338325103329935 0.5314904655067024 chr3 198022430 7516834 0.037959507920390635 0.21327513963712993 chr4 191154276 6992058 0.03657808837088217 0.21864143437338787 chr5 180915260 6678767 0.03691654866482794 0.2129385512604716 chr6 171115067 6386612 0.03732349296862327 0.24510292062259248 chr7 159138663 6080413 0.0382082699789931 0.5592601915081452 chr8 146364022 5629774 0.03846419306515094 0.4701694976932636 chr9 141213431 4619020 0.03270949489216787 0.34739060809132166 chr10 135534747 5240743 0.03866715448253281 0.34990782263184206 chr11 135006516 5115696 0.03789221551350899 0.3461764038428643 chr12 133851895 5094385 0.03805986459885383 0.214852356962139 chr13 115169878 3477344 0.030193172558540003 0.18808000536700886 chr14 107349540 3429213 0.03194436604013394 0.22522276915139977 chr15 102531392 3307315 0.032256608785726816 0.19606747644666683 chr16 90354753 3150870 0.03487221087306829 0.22566729806190763 chr17 81195210 3112477 0.03833325882154871 0.2684692529367622 chr18 78077248 2961162 0.03792605497570816 0.6039269430112871 chr19 59128983 2219318 0.03753350535388034 0.39088947997709156 chr20 63025520 2226085 0.03532037498460941 0.21250001300703178 chr21 48129895 1425355 0.029614753990217516 0.201111574648274 chr22 51304566 1249886 0.02436208114498035 0.1701530952038106 chrMT 16571 4479 0.2702914730553376 0.594007156440331 chrX 155270560 6267695 0.04036628063942063 0.296449868967359 chrY 59373566 241611 0.004069336175630751 0.1019904161551046