BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716332.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 = 996,179 number of mapped reads = 875,669 (87.9%) number of supplementary alignments = 3,237 (0.32%) number of secondary alignments = 0 number of mapped bases = 49,245,197 bp number of sequenced bases = 49,230,461 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,893 duplication rate = 2.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7703 >>>>>>> ACTG content number of A's = 11,859,478 bp (24.09%) number of C's = 9,301,753 bp (18.89%) number of T's = 16,380,568 bp (33.27%) number of G's = 11,687,919 bp (23.74%) number of N's = 743 bp (0%) GC percentage = 42.64% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 273,534 number of insertions = 3,678 mapped reads with insertion percentage = 0.42% number of deletions = 8,829 mapped reads with deletion percentage = 1% homopolymer indels = 40.75% >>>>>>> Coverage mean coverageData = 0.0159X std coverageData = 0.1773X There is a 1.48% of reference with a coverageData >= 1X There is a 0.07% 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 3963859 0.01590310581412754 0.322713418072156 chr2 243199373 4167909 0.01713782790056782 0.180542994216525 chr3 198022430 3347168 0.0169029740721796 0.1364989608350275 chr4 191154276 3241668 0.016958386010679668 0.14450512084750955 chr5 180915260 3038144 0.01679318814786547 0.13668855432874458 chr6 171115067 2854370 0.01668099747171884 0.14592095854984494 chr7 159138663 2639424 0.016585686659941336 0.17775587701506776 chr8 146364022 2524653 0.01724913653985267 0.1875017732793199 chr9 141213431 2087816 0.014784825956108949 0.17093636679312163 chr10 135534747 2315907 0.017087182816669145 0.17800247558825125 chr11 135006516 2212367 0.016387112752394854 0.1621613256188236 chr12 133851895 2259757 0.0168825178007379 0.14055867727234603 chr13 115169878 1587562 0.013784524456993867 0.1227983848057739 chr14 107349540 1495933 0.013935159852571329 0.1331528352237729 chr15 102531392 1374013 0.013400900672449662 0.12133793273224468 chr16 90354753 1411658 0.015623505716406529 0.14057927440692047 chr17 81195210 1273188 0.015680580172155477 0.1357100932819401 chr18 78077248 1328260 0.017012126247072643 0.27100517317799 chr19 59128983 966692 0.01634886904785763 0.22630076302791627 chr20 63025520 999318 0.0158557676319053 0.13449775788042537 chr21 48129895 644120 0.013382950451065809 0.12925425085527767 chr22 51304566 546113 0.01064453015741328 0.10799401557243118 chrMT 16571 9417 0.5682819383259912 0.8116891464421847 chrX 155270560 2808045 0.01808485137169596 0.15798356270245686 chrY 59373566 147836 0.002489929609415746 0.0728821802846244