BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525059.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 = 1,656,994 number of mapped reads = 1,511,416 (91.21%) number of supplementary alignments = 4,031 (0.24%) number of secondary alignments = 0 number of mapped bases = 88,717,290 bp number of sequenced bases = 88,689,684 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 186,513 duplication rate = 9.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2202 >>>>>>> ACTG content number of A's = 22,857,353 bp (25.77%) number of C's = 17,393,909 bp (19.61%) number of T's = 27,769,558 bp (31.31%) number of G's = 20,659,862 bp (23.29%) number of N's = 9,002 bp (0.01%) GC percentage = 42.91% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 427,227 number of insertions = 5,833 mapped reads with insertion percentage = 0.38% number of deletions = 17,249 mapped reads with deletion percentage = 1.13% homopolymer indels = 45.07% >>>>>>> Coverage mean coverageData = 0.0287X std coverageData = 0.2989X There is a 2.18% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 6699209 0.026877401440857394 0.4869310541203064 chr2 243199373 8289151 0.03408376797089851 0.3847581622329444 chr3 198022430 5456547 0.027555196651207644 0.21049802898538914 chr4 191154276 5757049 0.03011729122920588 0.2806965862268327 chr5 180915260 5139334 0.028407410187509887 0.21383248928517837 chr6 171115067 4651436 0.027183088441884547 0.22074331504737849 chr7 159138663 4566031 0.028692153835677255 0.2991773030800314 chr8 146364022 5458709 0.037295429063844664 0.3820281043397681 chr9 141213431 4697352 0.03326420133506989 0.2644779398780072 chr10 135534747 4141506 0.0305567840843057 0.3572756494079947 chr11 135006516 3734413 0.027660983415052354 0.25310847930222485 chr12 133851895 3715543 0.02775861335396111 0.21859999241256353 chr13 115169878 2593318 0.022517328706382757 0.19114644729696684 chr14 107349540 3385802 0.031539976789839996 0.22810793758444725 chr15 102531392 2821267 0.02751612891396227 0.20949409851067977 chr16 90354753 2491202 0.027571344254573967 0.22424302463978338 chr17 81195210 2246548 0.02766847945833258 0.2222937526858032 chr18 78077248 2181704 0.02794289061007888 0.41116013568240467 chr19 59128983 1712530 0.028962615507863547 0.3557893777097681 chr20 63025520 1842345 0.02923173025783841 0.226389821822538 chr21 48129895 1155248 0.02400271182806445 0.251344171782612 chr22 51304566 1050360 0.020473031581633494 0.18265370940009806 chrMT 16571 18502 1.1165288757467866 1.2551909454693668 chrX 155270560 4576201 0.029472431863451772 0.23235155268497276 chrY 59373566 335983 0.005658797721531498 0.23356058933309978