BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085125.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,380,220 number of mapped reads = 2,140,436 (89.93%) number of supplementary alignments = 18,998 (0.8%) number of secondary alignments = 0 number of mapped bases = 143,639,949 bp number of sequenced bases = 143,587,929 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,165 duplication rate = 2.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7658 >>>>>>> ACTG content number of A's = 40,385,815 bp (28.13%) number of C's = 26,719,612 bp (18.61%) number of T's = 44,900,451 bp (31.27%) number of G's = 31,554,713 bp (21.98%) number of N's = 27,338 bp (0.02%) GC percentage = 40.58% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,278,911 number of insertions = 11,472 mapped reads with insertion percentage = 0.53% number of deletions = 31,908 mapped reads with deletion percentage = 1.48% homopolymer indels = 46.65% >>>>>>> Coverage mean coverageData = 0.0464X std coverageData = 0.4094X There is a 4.08% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.05% 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 11329218 0.04545311844980318 0.7179718792414194 chr2 243199373 12081890 0.04967895209170626 0.5001745222819807 chr3 198022430 9921937 0.050105116879941326 0.2467409257470781 chr4 191154276 9663093 0.05055127827744748 0.2563455747212078 chr5 180915260 8944863 0.04944228032505384 0.24643238940112194 chr6 171115067 8460946 0.04944594388055845 0.3030283350390834 chr7 159138663 7980847 0.05015027052225517 0.5391431685305496 chr8 146364022 7419122 0.0506895198602837 0.6551856551313965 chr9 141213431 5957226 0.04218597308920283 0.3756856345536327 chr10 135534747 6694576 0.04939379862493859 0.3643777147626255 chr11 135006516 6510417 0.04822298354843851 0.3513139156308209 chr12 133851895 6590910 0.04924031893608977 0.2510470471855177 chr13 115169878 4617564 0.04009350431021556 0.22064627118315527 chr14 107349540 4413175 0.041110329862615154 0.24330299583801368 chr15 102531392 3990097 0.03891585710647526 0.2238408759047126 chr16 90354753 3834741 0.042440943864901055 0.2612252903772882 chr17 81195210 3593877 0.04426217999805654 0.26142499295915606 chr18 78077248 3969489 0.05084053423604275 0.6938013787208147 chr19 59128983 2633605 0.044540001643525645 0.5330144808774784 chr20 63025520 2775659 0.04404023957279527 0.23948814807147326 chr21 48129895 1882358 0.03910995442645366 0.23379162638458942 chr22 51304566 1463609 0.02852785071800432 0.1845838379810475 chrMT 16571 1469 0.08864884436666466 0.29527435363674526 chrX 155270560 8542839 0.05501905190526781 0.2977107820078168 chrY 59373566 366422 0.006171466945407995 0.13199404979886425