BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717002.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 = 1,928,443 number of mapped reads = 1,762,445 (91.39%) number of supplementary alignments = 7,606 (0.39%) number of secondary alignments = 0 number of mapped bases = 101,784,128 bp number of sequenced bases = 101,755,586 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,708 duplication rate = 3.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0175 >>>>>>> ACTG content number of A's = 26,383,470 bp (25.93%) number of C's = 17,991,173 bp (17.68%) number of T's = 31,826,056 bp (31.28%) number of G's = 25,553,176 bp (25.11%) number of N's = 1,711 bp (0%) GC percentage = 42.79% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 530,300 number of insertions = 5,634 mapped reads with insertion percentage = 0.32% number of deletions = 17,032 mapped reads with deletion percentage = 0.96% homopolymer indels = 44.87% >>>>>>> Coverage mean coverageData = 0.0329X std coverageData = 0.2993X There is a 2.9% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 7480835 0.030013305363038593 0.5001104029392908 chr2 243199373 6355908 0.026134557509735028 0.3156066515300569 chr3 198022430 6174954 0.03118310385343721 0.19332865263147408 chr4 191154276 6425300 0.033613163850961934 0.22999619582696343 chr5 180915260 5803874 0.032080621612571546 0.19949941280755568 chr6 171115067 5470894 0.03197201798717117 0.2195888715564518 chr7 159138663 6529551 0.04103057595752203 0.406432390928296 chr8 146364022 4495569 0.030714986774550375 0.2776516081925483 chr9 141213431 4799548 0.03398790020192909 0.32697016789038624 chr10 135534747 3966950 0.029268878186639476 0.2883180006443935 chr11 135006516 4037653 0.029907097224848023 0.25984031326809703 chr12 133851895 7758019 0.057959724813757774 0.29727337304274853 chr13 115169878 3866920 0.03357579314271741 0.20085735305183483 chr14 107349540 3747403 0.034908421591745994 0.2280085540108435 chr15 102531392 2636635 0.025715392608733918 0.17485757401921784 chr16 90354753 2999381 0.03319560842582349 0.21406297370798208 chr17 81195210 3126853 0.03851031360101168 0.22667149028532882 chr18 78077248 3295045 0.04220237116963958 0.5723896563621849 chr19 59128983 1753825 0.029661003978370473 0.37877850548872327 chr20 63025520 3074556 0.04878271531912787 0.2502685199998495 chr21 48129895 1275516 0.026501532986930473 0.20529441226246042 chr22 51304566 1017469 0.019831938545196933 0.15384362899997356 chrMT 16571 4545 0.2742743346810693 0.5682241747265078 chrX 155270560 5397923 0.034764626339983576 0.23927929874917198 chrY 59373566 289002 0.00486751966354859 0.12094086640072489