BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525125.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 = 1,863,357 number of mapped reads = 1,601,795 (85.96%) number of supplementary alignments = 47,623 (2.56%) number of secondary alignments = 0 number of mapped bases = 120,398,237 bp number of sequenced bases = 120,349,944 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,368 duplication rate = 1.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.249 >>>>>>> ACTG content number of A's = 31,488,769 bp (26.16%) number of C's = 23,496,145 bp (19.52%) number of T's = 36,890,815 bp (30.65%) number of G's = 28,469,293 bp (23.66%) number of N's = 4,922 bp (0%) GC percentage = 43.18% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 919,695 number of insertions = 10,648 mapped reads with insertion percentage = 0.66% number of deletions = 27,788 mapped reads with deletion percentage = 1.71% homopolymer indels = 41.67% >>>>>>> Coverage mean coverageData = 0.0389X std coverageData = 0.3821X There is a 3.44% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9708522 0.038950843777436364 0.5510715031213337 chr2 243199373 10211852 0.04198963128083393 0.6089865487618451 chr3 198022430 7918135 0.03998605107512316 0.21823189335216983 chr4 191154276 7639797 0.03996665499651182 0.2468539086861736 chr5 180915260 7229494 0.039960664456939674 0.22385379770727779 chr6 171115067 6839434 0.039969794126895906 0.2604700796598783 chr7 159138663 6826399 0.0428959177569564 0.5587217310682305 chr8 146364022 6125000 0.04184771582732265 0.5181794550535661 chr9 141213431 5110329 0.03618868944555281 0.37326506349132377 chr10 135534747 5218478 0.03850287926534441 0.363345571949054 chr11 135006516 5455113 0.04040629416731264 0.38470548566452756 chr12 133851895 5522973 0.04126182150801825 0.2249261668173034 chr13 115169878 3785831 0.03287171147302943 0.19734691887592049 chr14 107349540 3671328 0.034199755304028315 0.24144288161070485 chr15 102531392 3488459 0.03402332624139152 0.20261808700290934 chr16 90354753 3616702 0.040027800197738356 0.24367103316728095 chr17 81195210 3425296 0.04218593683051008 0.2650943853784492 chr18 78077248 3277873 0.04198243513910736 0.6205764788404201 chr19 59128983 2689795 0.045490297034197255 0.43677566231084564 chr20 63025520 2558947 0.04060175941428171 0.23106758899096258 chr21 48129895 1545946 0.032120286154790074 0.22057458182584977 chr22 51304566 1436209 0.027993785192530426 0.1826840707191 chrMT 16571 518 0.03125942912316698 0.17401803703656893 chrX 155270560 6780360 0.043668033399248386 0.3103942946335935 chrY 59373566 315447 0.005312919894351638 0.1369305234102213