BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524507.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,259,202 number of mapped reads = 1,151,887 (91.48%) number of supplementary alignments = 2,365 (0.19%) number of secondary alignments = 0 number of mapped bases = 66,536,304 bp number of sequenced bases = 66,515,764 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,383 duplication rate = 3.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2361 >>>>>>> ACTG content number of A's = 16,357,027 bp (24.59%) number of C's = 11,637,329 bp (17.5%) number of T's = 22,043,964 bp (33.14%) number of G's = 16,476,238 bp (24.77%) number of N's = 1,206 bp (0%) GC percentage = 42.27% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 313,165 number of insertions = 4,125 mapped reads with insertion percentage = 0.36% number of deletions = 11,955 mapped reads with deletion percentage = 1.03% homopolymer indels = 43.31% >>>>>>> Coverage mean coverageData = 0.0215X std coverageData = 0.2138X There is a 1.93% of reference with a coverageData >= 1X There is a 0.16% 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 6543057 0.026250915539343833 0.35427015253851035 chr2 243199373 5211879 0.02143047877018992 0.24875889618481486 chr3 198022430 3678897 0.018578183289640473 0.14917127179106351 chr4 191154276 3808062 0.019921406309529797 0.17393364995982585 chr5 180915260 3652324 0.02018803720592724 0.15535916975284594 chr6 171115067 2878988 0.016824865574227896 0.1710580062325305 chr7 159138663 3344162 0.021014139097046455 0.26372976002538373 chr8 146364022 6151906 0.04203154515663692 0.2519207336003718 chr9 141213431 2836463 0.020086354250538677 0.192757267824288 chr10 135534747 3473960 0.02563150835409019 0.22302693107812843 chr11 135006516 2274070 0.016844149951991946 0.20496631929368375 chr12 133851895 3057331 0.022841148420050385 0.16591648657520708 chr13 115169878 1501409 0.01303647295693063 0.12623713955266175 chr14 107349540 1602368 0.014926640579922374 0.13696326054500285 chr15 102531392 1759436 0.01715997379612285 0.14973166590416548 chr16 90354753 2068921 0.02289775503010893 0.1734367996212602 chr17 81195210 2284371 0.028134307430204317 0.19035161521832952 chr18 78077248 1586591 0.020320785384238954 0.30997971718798334 chr19 59128983 1364020 0.02306855167794785 0.26335839246974163 chr20 63025520 1920741 0.030475607341280166 0.19263719867379034 chr21 48129895 896317 0.018622874618779036 0.1584395994193197 chr22 51304566 539995 0.010525281511980825 0.11118885184928315 chrMT 16571 3941 0.2378251161667974 0.5582226517684112 chrX 155270560 3880330 0.024990764508094773 0.1889674451261956 chrY 59373566 216765 0.003650867121573934 0.09972011639354926