BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524365.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 = 1,257,991 number of mapped reads = 1,167,644 (92.82%) number of supplementary alignments = 5,501 (0.44%) number of secondary alignments = 0 number of mapped bases = 69,841,314 bp number of sequenced bases = 69,820,678 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,463 duplication rate = 2.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6439 >>>>>>> ACTG content number of A's = 18,121,483 bp (25.95%) number of C's = 14,153,645 bp (20.27%) number of T's = 21,385,553 bp (30.63%) number of G's = 16,149,566 bp (23.13%) number of N's = 10,431 bp (0.01%) GC percentage = 43.4% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 353,493 number of insertions = 5,560 mapped reads with insertion percentage = 0.47% number of deletions = 12,961 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.52% >>>>>>> Coverage mean coverageData = 0.0226X std coverageData = 0.2438X There is a 2.04% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5623113 0.022560076189338762 0.45889644041136163 chr2 243199373 5875588 0.024159552417925025 0.2886301064042539 chr3 198022430 4596887 0.023213971265780346 0.1644700737840863 chr4 191154276 4391624 0.022974238881268864 0.18896095675142965 chr5 180915260 4165466 0.02302440380098395 0.16473395739826813 chr6 171115067 3949898 0.02308328582193174 0.17126767784178656 chr7 159138663 3876978 0.02436226324208844 0.32725172102007255 chr8 146364022 3610129 0.024665412651751262 0.22482914543144436 chr9 141213431 2933305 0.020772138876789983 0.19652659790138735 chr10 135534747 3411642 0.02517171482232523 0.2404825911277874 chr11 135006516 3176163 0.02352599781183895 0.20928444166877425 chr12 133851895 3160140 0.023609228692653174 0.1681798577336667 chr13 115169878 2107427 0.01829842174531087 0.14612716503699033 chr14 107349540 2117061 0.019721193029797798 0.16173439693886457 chr15 102531392 2019257 0.019694036729746144 0.15115489069305518 chr16 90354753 2097647 0.023215679644434422 0.17814282497553693 chr17 81195210 1973789 0.024309180307557552 0.17752671991354155 chr18 78077248 1866958 0.02391167782962842 0.39382809321736895 chr19 59128983 1485862 0.025129165505856917 0.314510474447569 chr20 63025520 1537979 0.024402480138204334 0.17376467943082202 chr21 48129895 921981 0.019156098304390648 0.17782076953308082 chr22 51304566 859167 0.016746404208935323 0.1406673528204309 chrMT 16571 10246 0.6183090942007121 0.9446962315029702 chrX 155270560 3837521 0.02471505866920297 0.18489303455128808 chrY 59373566 235486 0.003966175789407697 0.127989061459133