BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230376.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 = 2,290,046 number of mapped reads = 1,486,352 (64.9%) number of supplementary alignments = 12,658 (0.55%) number of secondary alignments = 0 number of mapped bases = 93,186,217 bp number of sequenced bases = 93,142,633 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 423,641 duplication rate = 15.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1611 >>>>>>> ACTG content number of A's = 25,055,198 bp (26.9%) number of C's = 16,781,164 bp (18.02%) number of T's = 29,943,124 bp (32.15%) number of G's = 21,313,239 bp (22.88%) number of N's = 49,908 bp (0.05%) GC percentage = 40.9% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 878,590 number of insertions = 7,302 mapped reads with insertion percentage = 0.49% number of deletions = 27,245 mapped reads with deletion percentage = 1.81% homopolymer indels = 47.58% >>>>>>> Coverage mean coverageData = 0.0301X std coverageData = 0.5894X There is a 1.05% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 8315422 0.03336169020016203 0.660797232857757 chr2 243199373 8533090 0.03508680920817999 0.7785931616193877 chr3 198022430 5177933 0.02614821462396962 0.4604992264457176 chr4 191154276 5867086 0.03069293621242352 0.5112570653864084 chr5 180915260 5041630 0.027867356241811775 0.468142928543369 chr6 171115067 5408646 0.03160823938432026 0.570173059512271 chr7 159138663 5103464 0.03206929041498859 0.605666596101478 chr8 146364022 5163641 0.03527944182894892 0.5584972454712527 chr9 141213431 3460077 0.024502463933476697 0.43996598344994586 chr10 135534747 4819646 0.03556022427223035 0.5154715323833282 chr11 135006516 4032912 0.02987198040130152 0.5006490821624956 chr12 133851895 4146675 0.030979576344436512 0.4859256897154539 chr13 115169878 2677868 0.023251461636522704 0.4900598013899098 chr14 107349540 2793432 0.026021834839720787 0.8504781160572606 chr15 102531392 3038115 0.0296310714283485 1.0765177883175532 chr16 90354753 2481823 0.027467542299628663 0.462631876337666 chr17 81195210 2326981 0.028659092081909757 0.4723480480317416 chr18 78077248 2656656 0.03402599435881756 0.6230129094733396 chr19 59128983 1612145 0.027264886324867114 0.4651013056061672 chr20 63025520 1690143 0.02681680373283711 0.4157702603387369 chr21 48129895 1531296 0.03181590153063912 0.4800787342266636 chr22 51304566 937688 0.018276891768268733 0.3407735072538856 chrMT 16571 23219 1.4011827892100657 3.5490711844544327 chrX 155270560 6103050 0.03930590576861447 0.6412066928787424 chrY 59373566 243579 0.00410248223931842 0.2022071753547888