BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238277.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 = 1,461,617 number of mapped reads = 1,082,575 (74.07%) number of supplementary alignments = 11,945 (0.82%) number of secondary alignments = 0 number of mapped bases = 69,216,103 bp number of sequenced bases = 69,178,000 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 158,304 duplication rate = 10.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0293 >>>>>>> ACTG content number of A's = 19,130,946 bp (27.65%) number of C's = 13,276,286 bp (19.19%) number of T's = 21,262,646 bp (30.74%) number of G's = 15,493,568 bp (22.4%) number of N's = 14,554 bp (0.02%) GC percentage = 41.59% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 652,022 number of insertions = 5,604 mapped reads with insertion percentage = 0.51% number of deletions = 23,107 mapped reads with deletion percentage = 2.11% homopolymer indels = 46.99% >>>>>>> Coverage mean coverageData = 0.0224X std coverageData = 0.3142X There is a 1.18% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 5082852 0.02039253494979256 0.3958652675236421 chr2 243199373 5715017 0.023499308117048475 0.38183843317394606 chr3 198022430 4707841 0.02377428152962268 0.2673063606242886 chr4 191154276 4389093 0.02296099826717975 0.2864543434950693 chr5 180915260 4564034 0.025227468373867412 0.27540038490933505 chr6 171115067 4026176 0.02352905603572595 0.30439318740284227 chr7 159138663 4118866 0.02588224584996042 0.3391666560897049 chr8 146364022 3496702 0.023890447612870326 0.33824164582897087 chr9 141213431 2765439 0.019583399258955757 0.26854213109859026 chr10 135534747 2915551 0.02151146524809612 0.2795159381506218 chr11 135006516 3403160 0.025207375916581686 0.29440591650511116 chr12 133851895 3312804 0.02474977287396641 0.27655961007344076 chr13 115169878 2470341 0.021449540825249462 0.26715079446749174 chr14 107349540 2378547 0.02215703020245825 0.38070859303590115 chr15 102531392 1894752 0.018479725701958674 0.42171004499054093 chr16 90354753 2044043 0.022622418103450517 0.26110073133978373 chr17 81195210 1708027 0.021036056190999443 0.2537121468232131 chr18 78077248 1841929 0.02359111069078664 0.3782076379833743 chr19 59128983 1315099 0.02224119092323979 0.32015629217695607 chr20 63025520 1448964 0.022990115749937486 0.26592865419499645 chr21 48129895 920814 0.019131851419995825 0.23982209477136007 chr22 51304566 801468 0.015621767466076996 0.20746886093493513 chrMT 16571 14716 0.8880574497616318 1.9080192554818707 chrX 155270560 3704956 0.023861290897643442 0.28924587710922744 chrY 59373566 174912 0.0029459574653137727 0.10736087696425416