BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716920.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 = 1,041,351 number of mapped reads = 835,456 (80.23%) number of supplementary alignments = 3,637 (0.35%) number of secondary alignments = 0 number of mapped bases = 46,090,205 bp number of sequenced bases = 46,076,978 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,913 duplication rate = 1.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.9457 >>>>>>> ACTG content number of A's = 10,196,298 bp (22.13%) number of C's = 9,486,032 bp (20.59%) number of T's = 13,922,770 bp (30.22%) number of G's = 12,470,700 bp (27.06%) number of N's = 1,178 bp (0%) GC percentage = 47.65% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 249,665 number of insertions = 3,758 mapped reads with insertion percentage = 0.45% number of deletions = 7,754 mapped reads with deletion percentage = 0.92% homopolymer indels = 34.31% >>>>>>> Coverage mean coverageData = 0.0149X std coverageData = 0.149X There is a 1.37% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% 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 4412188 0.01770181346910265 0.17161242317501207 chr2 243199373 3857993 0.015863498957293776 0.18034778648067482 chr3 198022430 3052479 0.015414814372291058 0.13771319653332123 chr4 191154276 2865711 0.014991613370971622 0.15246235659394958 chr5 180915260 2669856 0.01475749475196288 0.13110838618843676 chr6 171115067 1979454 0.011567970224387079 0.11749598629150611 chr7 159138663 2605322 0.01637139555457997 0.1586018015752389 chr8 146364022 2714285 0.01854475548642685 0.153180206839936 chr9 141213431 2000898 0.014169317931238424 0.1361419282198616 chr10 135534747 2422087 0.017870598157386165 0.2115210018197772 chr11 135006516 1881230 0.013934364471711869 0.1443829896956543 chr12 133851895 2173897 0.01624106255649201 0.13647890865850348 chr13 115169878 800293 0.00694880479078045 0.09216356102124569 chr14 107349540 1992331 0.018559287724940414 0.14945612155075214 chr15 102531392 938359 0.009151919053239812 0.10517099862674616 chr16 90354753 1277454 0.014138204771585176 0.13903223672829976 chr17 81195210 1974380 0.02431645906205551 0.17841968270874706 chr18 78077248 1178399 0.015092732264333907 0.15708766625404094 chr19 59128983 1369499 0.023161213511823805 0.18104131456934408 chr20 63025520 1193154 0.018931283708567576 0.1567105952094642 chr21 48129895 609265 0.012658764370875939 0.13835836981343783 chr22 51304566 552544 0.01076987962435936 0.11964667991836851 chrMT 16571 8305 0.5011767545712389 0.8156608371985186 chrX 155270560 1399690 0.009014522778819114 0.10812891949626824 chrY 59373566 161132 0.0027138676494519462 0.09758714562491032