BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004159.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 = 1,335,745 number of mapped reads = 1,146,668 (85.84%) number of supplementary alignments = 9,519 (0.71%) number of secondary alignments = 0 number of mapped bases = 75,580,452 bp number of sequenced bases = 75,530,555 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,053 duplication rate = 2.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3245 >>>>>>> ACTG content number of A's = 21,790,125 bp (28.85%) number of C's = 13,608,023 bp (18.02%) number of T's = 23,936,420 bp (31.69%) number of G's = 16,181,898 bp (21.42%) number of N's = 14,089 bp (0.02%) GC percentage = 39.44% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 751,126 number of insertions = 5,888 mapped reads with insertion percentage = 0.51% number of deletions = 29,265 mapped reads with deletion percentage = 2.51% homopolymer indels = 43.68% >>>>>>> Coverage mean coverageData = 0.0244X std coverageData = 0.2607X There is a 2.19% of reference with a coverageData >= 1X There is a 0.18% 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 6318035 0.025348121399464837 0.5116198520145284 chr2 243199373 5395861 0.02218698565476976 0.2359563025237376 chr3 198022430 3578374 0.01807054887671058 0.14447234327955727 chr4 191154276 5519345 0.028873772093908064 0.1947043097643553 chr5 180915260 4587407 0.025356661455755585 0.17392277863921005 chr6 171115067 4914819 0.028722304155717627 0.19852519282142267 chr7 159138663 3503219 0.022013625940793532 0.24120004202421455 chr8 146364022 5934940 0.040549172664850655 0.46190734149914703 chr9 141213431 3067526 0.021722622120837785 0.22713545291590495 chr10 135534747 3597289 0.026541452134042055 0.246442590571458 chr11 135006516 1951052 0.014451539509396717 0.14601304320170178 chr12 133851895 4299644 0.03212239916364277 0.19587597996787884 chr13 115169878 3058127 0.026553184331757303 0.17506019595073463 chr14 107349540 1115740 0.010393523810162578 0.12302725965491608 chr15 102531392 2440622 0.02380365615244939 0.16557502719105394 chr16 90354753 2353121 0.026043134664979938 0.1938638653246768 chr17 81195210 711412 0.008761748383925603 0.10407341186195151 chr18 78077248 2438023 0.031225780396358233 0.3914244956441343 chr19 59128983 1384229 0.02341032992229885 0.34161085887211073 chr20 63025520 1896346 0.030088541911276575 0.19273102704327677 chr21 48129895 1277521 0.02654319108736888 0.18682229223362595 chr22 51304566 609058 0.011871419007813067 0.11578504012823347 chrMT 16571 19450 1.1737372518254783 1.3883127663536665 chrX 155270560 5396327 0.034754347507988635 0.21822122402025762 chrY 59373566 212965 0.0035868655758355492 0.09474848545968145