BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084878.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 = 2,347,753 number of mapped reads = 2,115,392 (90.1%) number of supplementary alignments = 15,700 (0.67%) number of secondary alignments = 0 number of mapped bases = 145,961,552 bp number of sequenced bases = 145,904,731 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,216 duplication rate = 3.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6471 >>>>>>> ACTG content number of A's = 42,341,557 bp (29.02%) number of C's = 26,512,966 bp (18.17%) number of T's = 47,040,791 bp (32.24%) number of G's = 29,985,936 bp (20.55%) number of N's = 23,481 bp (0.02%) GC percentage = 38.72% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,186,545 number of insertions = 11,563 mapped reads with insertion percentage = 0.54% number of deletions = 32,533 mapped reads with deletion percentage = 1.52% homopolymer indels = 49.29% >>>>>>> Coverage mean coverageData = 0.0471X std coverageData = 0.35X There is a 3.96% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% 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 12537615 0.05030123876802698 0.4947803108363171 chr2 243199373 12834921 0.05277530464685861 0.39066313489779325 chr3 198022430 10937439 0.05523333392080887 0.270873597372298 chr4 191154276 8628191 0.04513731620630867 0.2454788085872863 chr5 180915260 7966666 0.04403534560876733 0.24159352750894506 chr6 171115067 8726396 0.05099723918525538 0.26281142818315256 chr7 159138663 8882513 0.05581618465652184 0.3509376731577806 chr8 146364022 7828655 0.05348756404084058 0.6989056837617166 chr9 141213431 10281502 0.07280824442258613 0.41276205774411806 chr10 135534747 4508969 0.03326799289336483 0.2513255703484953 chr11 135006516 6326413 0.04686005673977988 0.31669890369074644 chr12 133851895 6462278 0.04827931647885897 0.2554473898606181 chr13 115169878 3665618 0.03182792292269338 0.20305984429375817 chr14 107349540 2856911 0.026613164807226933 0.20342678001010533 chr15 102531392 3485757 0.03399697333671233 0.2107017847921344 chr16 90354753 2465612 0.027288127277598776 0.20323584564901548 chr17 81195210 3569161 0.04395777780487297 0.25227083388516836 chr18 78077248 6248509 0.08002983148176535 0.6553554060194902 chr19 59128983 2444555 0.04134275402639683 0.33806201619628135 chr20 63025520 2668449 0.04233918260412607 0.24442155252182493 chr21 48129895 1325114 0.027532035962264202 0.2020772370745668 chr22 51304566 1316663 0.02566366120317634 0.18015028103279745 chrMT 16571 48855 2.948222798865488 2.1612932452206315 chrX 155270560 9614955 0.061923876618980446 0.30702960201240476 chrY 59373566 329835 0.005555249957531606 0.12653110220933209