BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714222.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 226,286 number of mapped reads = 21,247 (9.39%) number of supplementary alignments = 624 (0.28%) number of secondary alignments = 0 number of mapped bases = 2,226,172 bp number of sequenced bases = 2,190,675 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,814 duplication rate = 38.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 32.5041 >>>>>>> ACTG content number of A's = 474,523 bp (21.66%) number of C's = 328,189 bp (14.98%) number of T's = 432,040 bp (19.72%) number of G's = 955,838 bp (43.63%) number of N's = 85 bp (0%) GC percentage = 58.61% >>>>>>> Mismatches and indels general error rate = 0.0379 number of mismatches = 73,075 number of insertions = 2,202 mapped reads with insertion percentage = 9.13% number of deletions = 5,767 mapped reads with deletion percentage = 26.09% homopolymer indels = 31.69% >>>>>>> Coverage mean coverageData = 0.0007X std coverageData = 0.7518X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% 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 67815 2.720755508167821E-4 0.07939260923866716 chr2 243199373 763875 0.003140941485897663 2.6133625004390515 chr3 198022430 77892 3.933493796637078E-4 0.1804534955945703 chr4 191154276 63301 3.3115136801857364E-4 0.14307322063966094 chr5 180915260 76706 4.2398855685252864E-4 0.17025933786566058 chr6 171115067 91786 5.363992873871241E-4 0.14328570557589457 chr7 159138663 68724 4.3184980132703515E-4 0.15542955803266847 chr8 146364022 81086 5.540022670325362E-4 0.25620482060308536 chr9 141213431 60004 4.2491708880014397E-4 0.11694306823605875 chr10 135534747 37391 2.7587759469532933E-4 0.08220778637413381 chr11 135006516 34819 2.5790607025219433E-4 0.10590918838120855 chr12 133851895 51290 3.831847132235222E-4 0.1039813124428426 chr13 115169878 14560 1.2642194515479125E-4 0.03793288015871632 chr14 107349540 44022 4.1008093746838596E-4 0.12200438885333657 chr15 102531392 51544 5.027143296757349E-4 0.12496188791486414 chr16 90354753 36175 4.0036632051885525E-4 0.11928011731232935 chr17 81195210 31776 3.91353135240367E-4 0.10284250800939797 chr18 78077248 29213 3.741550931713167E-4 0.1441273078608899 chr19 59128983 3539 5.985220479777236E-5 0.013077820559739559 chr20 63025520 41706 6.61731946043444E-4 0.21041712997526718 chr21 48129895 2453 5.096624457626596E-5 0.017696631078143475 chr22 51304566 15715 3.063080194460665E-4 0.10714838001658228 chrMT 16571 648 0.039104459598093055 0.33402007740047857 chrX 155270560 479241 0.0030864898020590637 0.49649687979156426 chrY 59373566 891 1.5006678224447559E-5 0.0061477129354606365