BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819131.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,099,031 number of mapped reads = 1,003,119 (91.27%) number of supplementary alignments = 4,379 (0.4%) number of secondary alignments = 0 number of mapped bases = 58,355,518 bp number of sequenced bases = 58,336,838 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,581 duplication rate = 2.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8007 >>>>>>> ACTG content number of A's = 14,879,699 bp (25.51%) number of C's = 10,944,774 bp (18.76%) number of T's = 18,796,453 bp (32.22%) number of G's = 13,714,956 bp (23.51%) number of N's = 956 bp (0%) GC percentage = 42.27% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 299,740 number of insertions = 4,111 mapped reads with insertion percentage = 0.41% number of deletions = 11,195 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.34% >>>>>>> Coverage mean coverageData = 0.0189X std coverageData = 0.2039X There is a 1.71% of reference with a coverageData >= 1X There is a 0.12% 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 5738729 0.02302393060035746 0.3764220200327525 chr2 243199373 4660888 0.019164884935784766 0.22839693241160877 chr3 198022430 3125294 0.01578252524221625 0.13559323571099355 chr4 191154276 3356163 0.017557352470629534 0.16209326689528794 chr5 180915260 3182455 0.017590859941831332 0.1427737114141527 chr6 171115067 2523609 0.014748023328652876 0.15334455100525857 chr7 159138663 2964436 0.01862800619356718 0.2390399741505154 chr8 146364022 5320858 0.03635359241494471 0.23395432791475523 chr9 141213431 2469580 0.017488279850660947 0.16709328267669293 chr10 135534747 3095706 0.022840681585512532 0.22470244316453342 chr11 135006516 1975655 0.014633775157933859 0.16877145519427109 chr12 133851895 2713581 0.02027301145045425 0.15456495468669176 chr13 115169878 1270222 0.011029116484780856 0.1139153653800256 chr14 107349540 1386806 0.012918602166343702 0.12375191277412041 chr15 102531392 1544495 0.015063630463536475 0.1331468831281585 chr16 90354753 1825659 0.02020545615347983 0.16155973235588197 chr17 81195210 2049176 0.025237646407959287 0.17663779849928019 chr18 78077248 1368782 0.01753112507244108 0.28661944000025663 chr19 59128983 1228811 0.020781872740818153 0.26441438705809356 chr20 63025520 1673597 0.026554275157110962 0.17658208821073515 chr21 48129895 815479 0.016943294806689272 0.15145444676266653 chr22 51304566 493171 0.009612614206696535 0.10600884913388907 chrMT 16571 17861 1.0778468408665742 1.2598028856779586 chrX 155270560 3342558 0.02152731335547447 0.16686720889553322 chrY 59373566 211947 0.003569719898582477 0.12119303925868495