BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237294.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 = 2,577,476 number of mapped reads = 2,288,019 (88.77%) number of supplementary alignments = 15,921 (0.62%) number of secondary alignments = 0 number of mapped bases = 154,677,505 bp number of sequenced bases = 154,612,792 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 143,771 duplication rate = 4.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5224 >>>>>>> ACTG content number of A's = 44,186,529 bp (28.58%) number of C's = 27,792,756 bp (17.98%) number of T's = 49,748,023 bp (32.18%) number of G's = 32,883,072 bp (21.27%) number of N's = 2,412 bp (0%) GC percentage = 39.24% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,202,752 number of insertions = 12,844 mapped reads with insertion percentage = 0.56% number of deletions = 36,838 mapped reads with deletion percentage = 1.59% homopolymer indels = 47.48% >>>>>>> Coverage mean coverageData = 0.05X std coverageData = 0.6175X There is a 3.83% of reference with a coverageData >= 1X There is a 0.8% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% 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% 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 15917951 0.06386323506893088 0.9528986476687309 chr2 243199373 10829781 0.04453046431168225 0.5624267786678468 chr3 198022430 9540840 0.04818060257113298 0.27058500434120786 chr4 191154276 8046276 0.04209309971177417 0.33964512414580933 chr5 180915260 7879115 0.04355141185989507 0.26509907080761813 chr6 171115067 12685616 0.07413500296849955 0.46509576291063703 chr7 159138663 8792488 0.05525048303315204 0.6812435417672043 chr8 146364022 9206404 0.06290073116465739 1.7155860842424053 chr9 141213431 7750430 0.05488451024180554 0.5612118509095795 chr10 135534747 6909705 0.05098105949170363 0.47931288392344457 chr11 135006516 5865761 0.04344798439210149 0.43498649676815493 chr12 133851895 4184532 0.03126240386809615 0.23940140654662626 chr13 115169878 6512283 0.05654501952324722 0.2956260214369863 chr14 107349540 5394663 0.050253247475489884 0.3193591784808665 chr15 102531392 3896887 0.03800676967303828 0.246335803994354 chr16 90354753 3502308 0.03876174615850037 0.29248803795000233 chr17 81195210 4459952 0.054928757496901605 0.3539422195978273 chr18 78077248 5184926 0.0664076428513464 0.9840862038391522 chr19 59128983 2603737 0.044034868653161176 0.605872879308895 chr20 63025520 2339988 0.037127627031082015 0.25594573636809065 chr21 48129895 2621142 0.05445974897722092 0.34840155945428825 chr22 51304566 1095661 0.021356013419936152 0.17286885503678037 chrMT 16571 59749 3.605636352664293 3.579811144236551 chrX 155270560 8974783 0.0578009314837275 0.3476868927665095 chrY 59373566 422527 0.007116416083211172 0.24661878597933032