BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819129.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 = 1,483,577 number of mapped reads = 1,367,051 (92.15%) number of supplementary alignments = 5,649 (0.38%) number of secondary alignments = 0 number of mapped bases = 80,902,662 bp number of sequenced bases = 80,876,494 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,012 duplication rate = 3.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5648 >>>>>>> ACTG content number of A's = 20,936,610 bp (25.89%) number of C's = 16,128,348 bp (19.94%) number of T's = 25,021,063 bp (30.94%) number of G's = 18,789,222 bp (23.23%) number of N's = 1,251 bp (0%) GC percentage = 43.17% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 409,260 number of insertions = 6,525 mapped reads with insertion percentage = 0.47% number of deletions = 15,701 mapped reads with deletion percentage = 1.14% homopolymer indels = 41.46% >>>>>>> Coverage mean coverageData = 0.0261X std coverageData = 0.2555X There is a 2.31% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% 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 8103714 0.032512312175944386 0.470628197183623 chr2 243199373 6514747 0.026787680081724552 0.2839604147895106 chr3 198022430 4492834 0.022688510589431714 0.16672269201458306 chr4 191154276 4607348 0.02410277235964107 0.2031417321718417 chr5 180915260 4464060 0.024674867117345435 0.17467469108242883 chr6 171115067 3391261 0.01981859960934942 0.19027532210846598 chr7 159138663 4134219 0.02597872146255244 0.3000539725044532 chr8 146364022 6523930 0.044573317341607355 0.2861877671443196 chr9 141213431 3525655 0.024966853188348636 0.21948817979016294 chr10 135534747 4307679 0.03178283868416414 0.2741420988236097 chr11 135006516 2789731 0.020663676707278335 0.2170886811180281 chr12 133851895 3717009 0.027769565757735443 0.1842405618142581 chr13 115169878 1793408 0.015571849437923344 0.13765725410399923 chr14 107349540 1938882 0.01806139085458587 0.15243266041684506 chr15 102531392 2196162 0.021419410749831624 0.16331104137762822 chr16 90354753 2549412 0.028215582637916126 0.19993964653393775 chr17 81195210 2886424 0.035549190648069016 0.22224222838840724 chr18 78077248 1929598 0.024713960205154772 0.39343640200750046 chr19 59128983 1689127 0.028566819760793113 0.3186425254625956 chr20 63025520 2326479 0.036913285285071824 0.21574127524958137 chr21 48129895 1138485 0.023654425175870422 0.19583371511768954 chr22 51304566 679666 0.013247670782362725 0.12627661485828262 chrMT 16571 2826 0.17053889324723914 0.4384826542287157 chrX 155270560 4897171 0.03153959771897519 0.21451074949981866 chrY 59373566 302835 0.005100502132548346 0.17717927627310304