BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008747.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,588,453 number of mapped reads = 1,173,068 (73.85%) number of supplementary alignments = 8,240 (0.52%) number of secondary alignments = 0 number of mapped bases = 75,302,957 bp number of sequenced bases = 75,264,609 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,278 duplication rate = 2.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4685 >>>>>>> ACTG content number of A's = 22,698,137 bp (30.16%) number of C's = 13,428,591 bp (17.84%) number of T's = 22,318,679 bp (29.65%) number of G's = 16,807,658 bp (22.33%) number of N's = 11,544 bp (0.02%) GC percentage = 40.17% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 694,866 number of insertions = 5,810 mapped reads with insertion percentage = 0.49% number of deletions = 24,365 mapped reads with deletion percentage = 2.05% homopolymer indels = 47.09% >>>>>>> Coverage mean coverageData = 0.0243X std coverageData = 0.2238X There is a 2.12% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.04% 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 5161292 0.02070723827805428 0.3212167630545122 chr2 243199373 6326695 0.02601443795663075 0.27783989970532535 chr3 198022430 4443238 0.022438054113364834 0.16949048161598568 chr4 191154276 4928970 0.025785298153623307 0.18408172142735815 chr5 180915260 2184595 0.012075238982051597 0.11930754208781003 chr6 171115067 4506633 0.026336856707071855 0.19582351122190533 chr7 159138663 4255832 0.026742916647477428 0.23901826682019786 chr8 146364022 8373872 0.057212639319244724 0.3371530916570341 chr9 141213431 2347946 0.01662693118758654 0.21307424481979237 chr10 135534747 3266187 0.024098521392451486 0.23053626816864525 chr11 135006516 3560094 0.02636979388461517 0.21375048154006698 chr12 133851895 3154581 0.023567697715448855 0.17157515554324929 chr13 115169878 2804976 0.02435511827146331 0.17749478836912008 chr14 107349540 2266516 0.021113420700265693 0.16685183388695193 chr15 102531392 1585772 0.015466209607297636 0.1384206226671764 chr16 90354753 2168612 0.024001083816808176 0.18812679152036216 chr17 81195210 1796769 0.022129002437459057 0.18767824271027805 chr18 78077248 1430126 0.018316808502266885 0.3367185986284596 chr19 59128983 1409067 0.023830394647579176 0.22507155406819365 chr20 63025520 2066569 0.032789400230255936 0.20460649006224335 chr21 48129895 644234 0.013385319041315175 0.13545813264588666 chr22 51304566 977951 0.019061675719077322 0.15421908114786656 chrMT 16571 16055 0.9688612636533703 1.3172398434519028 chrX 155270560 5420771 0.03491177593485848 0.22490748020065096 chrY 59373566 205604 0.003462887844735484 0.08289308037914866