BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237602.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 = 1,915,796 number of mapped reads = 1,587,963 (82.89%) number of supplementary alignments = 9,255 (0.48%) number of secondary alignments = 0 number of mapped bases = 101,090,167 bp number of sequenced bases = 101,033,136 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,892 duplication rate = 3.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.4716 >>>>>>> ACTG content number of A's = 25,815,773 bp (25.55%) number of C's = 19,467,465 bp (19.27%) number of T's = 30,352,961 bp (30.04%) number of G's = 25,372,675 bp (25.11%) number of N's = 24,262 bp (0.02%) GC percentage = 44.38% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 922,746 number of insertions = 9,598 mapped reads with insertion percentage = 0.6% number of deletions = 34,268 mapped reads with deletion percentage = 2.13% homopolymer indels = 45.88% >>>>>>> Coverage mean coverageData = 0.0327X std coverageData = 0.3064X There is a 2.7% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 9002636 0.036118810713013226 0.38893563273273757 chr2 243199373 8982621 0.036935214467020853 0.4406242227113592 chr3 198022430 6779860 0.03423783861252486 0.23193416478521411 chr4 191154276 6248563 0.032688586050777124 0.24594396715949632 chr5 180915260 5526247 0.03054605233411488 0.21211573550341967 chr6 171115067 5193454 0.030350652873834892 0.23948095013862486 chr7 159138663 5986940 0.03762090171638554 0.44640473917800744 chr8 146364022 5437465 0.03715028410465517 0.2973198517861476 chr9 141213431 4111065 0.02911242203300053 0.3207020016805762 chr10 135534747 4507764 0.033259102184327684 0.31299246194249025 chr11 135006516 4181611 0.030973401313459565 0.3201643832416602 chr12 133851895 5693879 0.04253865064816602 0.2673529350417986 chr13 115169878 3188642 0.02768642335455109 0.20867774449764584 chr14 107349540 2893626 0.02695517838269265 0.2336298402747745 chr15 102531392 2911425 0.028395449854031047 0.22120799981106634 chr16 90354753 2716080 0.03006017846122605 0.24678432270924977 chr17 81195210 2749295 0.03386031023258638 0.24647309433117284 chr18 78077248 2472171 0.03166314212304204 0.45826991870533645 chr19 59128983 2161535 0.036556268860568765 0.3213724617536001 chr20 63025520 2225963 0.03531843926079468 0.2429258797196718 chr21 48129895 1300699 0.02702476288385836 0.23098794196303124 chr22 51304566 1111695 0.021668539209551058 0.18601036687080025 chrMT 16571 85962 5.187496228350733 4.5319719180851505 chrX 155270560 5259627 0.03387394880265776 0.26037368539457495 chrY 59373566 361342 0.006085906984262997 0.1514204157198334