BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004032.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,362,043 number of mapped reads = 2,124,449 (89.94%) number of supplementary alignments = 27,784 (1.18%) number of secondary alignments = 0 number of mapped bases = 141,859,320 bp number of sequenced bases = 141,779,924 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 120,793 duplication rate = 4.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.0548 >>>>>>> ACTG content number of A's = 40,592,684 bp (28.63%) number of C's = 26,491,396 bp (18.68%) number of T's = 44,641,418 bp (31.49%) number of G's = 30,043,798 bp (21.19%) number of N's = 10,628 bp (0.01%) GC percentage = 39.88% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,313,685 number of insertions = 11,257 mapped reads with insertion percentage = 0.53% number of deletions = 47,466 mapped reads with deletion percentage = 2.2% homopolymer indels = 44.36% >>>>>>> Coverage mean coverageData = 0.0458X std coverageData = 0.4511X There is a 3.53% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 13273260 0.05325266571753095 0.7276387871398505 chr2 243199373 16161033 0.06645178727496144 0.5299620273959125 chr3 198022430 799364 0.004036734626476405 0.089082632964676 chr4 191154276 17461798 0.0913492408613449 0.39861751598665635 chr5 180915260 752248 0.0041580129835371545 0.10413369545923185 chr6 171115067 5343641 0.031228348816296814 0.2186962856910777 chr7 159138663 9614375 0.060415079646609825 0.559345749839392 chr8 146364022 11942855 0.08159693097255827 0.7141756452125638 chr9 141213431 10721326 0.07592284901002087 0.5661014865608232 chr10 135534747 6357170 0.046904355825447476 0.39362057723527044 chr11 135006516 9747747 0.07220204838113146 0.5508151286715358 chr12 133851895 855706 0.006392931530778851 0.1422361202990616 chr13 115169878 4617295 0.04009116863004752 0.24369809707741666 chr14 107349540 412911 0.0038464161094681915 0.20929015012362961 chr15 102531392 6863891 0.06694428765777412 0.3178356481011824 chr16 90354753 1725695 0.019099105942993393 0.2824559869579042 chr17 81195210 1852365 0.022813722632160197 0.25922430900226134 chr18 78077248 3637765 0.046591870143783756 0.937058590630883 chr19 59128983 2482128 0.04197819536317748 0.4368884133004576 chr20 63025520 4735408 0.0751347708039537 0.35228955438780835 chr21 48129895 3175095 0.06596928998079052 0.3673512941402014 chr22 51304566 778823 0.015180383749859612 0.15003526984660884 chrMT 16571 8804 0.5312896023173013 0.7631420174973044 chrX 155270560 8130316 0.052362250770525975 0.34170551908980684 chrY 59373566 408301 0.006876814506981103 0.21073984504221174