BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524653.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 = 1,189,758 number of mapped reads = 1,099,808 (92.44%) number of supplementary alignments = 4,183 (0.35%) number of secondary alignments = 0 number of mapped bases = 64,020,951 bp number of sequenced bases = 64,000,597 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,109 duplication rate = 3.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7991 >>>>>>> ACTG content number of A's = 15,702,078 bp (24.53%) number of C's = 11,966,785 bp (18.7%) number of T's = 20,618,510 bp (32.22%) number of G's = 15,712,625 bp (24.55%) number of N's = 599 bp (0%) GC percentage = 43.25% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 324,616 number of insertions = 4,152 mapped reads with insertion percentage = 0.38% number of deletions = 12,156 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.65% >>>>>>> Coverage mean coverageData = 0.0207X std coverageData = 0.2047X There is a 1.87% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 6139949 0.02463363571720048 0.33910952195941707 chr2 243199373 5614374 0.023085478925145092 0.2451941511003309 chr3 198022430 4015922 0.02028013695216244 0.1551503706701035 chr4 191154276 2860984 0.01496688465394308 0.1534015496565763 chr5 180915260 3938492 0.021769816432289903 0.15982286799665596 chr6 171115067 4209164 0.024598441702389656 0.18054671548904253 chr7 159138663 3913798 0.024593633792185373 0.25381728070468956 chr8 146364022 5831334 0.03984130744917627 0.2767949502905771 chr9 141213431 2354510 0.0166734140182459 0.17382594366527016 chr10 135534747 2824044 0.020836309968542605 0.2240218797357606 chr11 135006516 3284801 0.024330684898201504 0.18907805441141975 chr12 133851895 2145146 0.016026265448090965 0.14037825304932877 chr13 115169878 1541163 0.013381650017897909 0.12568366168950482 chr14 107349540 1166928 0.010870358643362608 0.11617310288463918 chr15 102531392 1667426 0.016262590095333925 0.13860763764326436 chr16 90354753 1937176 0.0214396690343451 0.16668801949567377 chr17 81195210 1485971 0.01830121505936126 0.15032779715945177 chr18 78077248 1701106 0.021787473861783653 0.25504184503193705 chr19 59128983 1276353 0.021585911599392806 0.2528256951332525 chr20 63025520 1234430 0.019586193021493517 0.15562674278620048 chr21 48129895 582193 0.012096286517973912 0.13921842782735322 chr22 51304566 1210812 0.023600472519346525 0.16727694651157576 chrMT 16571 3194 0.19274636413010682 0.4772520126872709 chrX 155270560 2903382 0.01869885701449135 0.15858644323099166 chrY 59373566 178299 0.003003003053581117 0.10486571035008202