BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524977.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 = 2,567,377 number of mapped reads = 2,378,238 (92.63%) number of supplementary alignments = 5,659 (0.22%) number of secondary alignments = 0 number of mapped bases = 138,453,497 bp number of sequenced bases = 138,411,261 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 135,848 duplication rate = 4.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8724 >>>>>>> ACTG content number of A's = 35,764,677 bp (25.84%) number of C's = 25,443,318 bp (18.38%) number of T's = 44,575,486 bp (32.21%) number of G's = 32,626,227 bp (23.57%) number of N's = 1,553 bp (0%) GC percentage = 41.95% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 661,272 number of insertions = 9,750 mapped reads with insertion percentage = 0.41% number of deletions = 24,998 mapped reads with deletion percentage = 1.04% homopolymer indels = 43.46% >>>>>>> Coverage mean coverageData = 0.0447X std coverageData = 0.3628X There is a 3.79% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 11880599 0.04766527341971998 0.6543101915121093 chr2 243199373 12228795 0.05028300381350079 0.42494158403864923 chr3 198022430 9501703 0.04798296334410198 0.25424954510806513 chr4 191154276 9086348 0.047534107999760364 0.2921647248829104 chr5 180915260 8606644 0.047572791814244966 0.2529396992009268 chr6 171115067 8168236 0.04773534057056472 0.3337920809479768 chr7 159138663 8043135 0.05054167760602588 0.4819346960100935 chr8 146364022 7455736 0.05093967696514926 0.36168429589696544 chr9 141213431 5675162 0.04018854268897411 0.29878345475521556 chr10 135534747 5976022 0.04409217659881713 0.36580023894072866 chr11 135006516 6540798 0.04844801713126202 0.3667068445454218 chr12 133851895 6207544 0.04637621305249358 0.2517867456073802 chr13 115169878 4253323 0.03693086312030304 0.22420107302754505 chr14 107349540 4118650 0.038366722391171865 0.23397111877478383 chr15 102531392 3973351 0.03875253151737177 0.24012674462563283 chr16 90354753 3434460 0.03801083934123532 0.2453637864695661 chr17 81195210 3359440 0.04137485450188502 0.25657153252288933 chr18 78077248 3486472 0.0446541353506722 0.515048559047006 chr19 59128983 2536013 0.04288950817909383 0.43163166551000376 chr20 63025520 2439941 0.038713540165951826 0.23442578892048996 chr21 48129895 1772949 0.03683675187739346 0.2493669493464951 chr22 51304566 1578613 0.030769444575361966 0.20148033653821143 chrMT 16571 33123 1.9988534186228955 1.8977699887174975 chrX 155270560 7699142 0.04958533027767788 0.2870316473838077 chrY 59373566 397298 0.006691496347044407 0.18069195551299042