BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716526.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 = 3,174,620 number of mapped reads = 2,985,707 (94.05%) number of supplementary alignments = 58,429 (1.84%) number of secondary alignments = 0 number of mapped bases = 235,827,327 bp number of sequenced bases = 235,725,522 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 158,615 duplication rate = 3.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4287 >>>>>>> ACTG content number of A's = 59,399,580 bp (25.2%) number of C's = 46,290,857 bp (19.64%) number of T's = 72,071,123 bp (30.57%) number of G's = 57,947,680 bp (24.58%) number of N's = 16,282 bp (0.01%) GC percentage = 44.22% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,458,460 number of insertions = 18,560 mapped reads with insertion percentage = 0.61% number of deletions = 52,894 mapped reads with deletion percentage = 1.74% homopolymer indels = 43.38% >>>>>>> Coverage mean coverageData = 0.0762X std coverageData = 0.5869X There is a 5.99% of reference with a coverageData >= 1X There is a 1.09% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 19081003 0.07655348228801404 0.9247604486234751 chr2 243199373 20141763 0.08281996269784792 0.7873265320864385 chr3 198022430 15461306 0.07807855908040316 0.3379453242512297 chr4 191154276 15454585 0.08084875380972383 0.44931105067027094 chr5 180915260 14469404 0.07997890282997687 0.35250704350466994 chr6 171115067 13509851 0.07895184940084791 0.3936147905490336 chr7 159138663 12761704 0.08019235401016282 0.8324371278351759 chr8 146364022 12068529 0.08245557094625344 0.762121418435751 chr9 141213431 9993396 0.07076802772393513 0.5980348487499578 chr10 135534747 11231566 0.08286853554978045 0.5766781963608054 chr11 135006516 10709182 0.0793234453957763 0.6190282006249714 chr12 133851895 10599871 0.07919104171069076 0.3488734068111194 chr13 115169878 7492960 0.06506006718180252 0.3080620703362883 chr14 107349540 7315398 0.0681455924263858 0.364307510361761 chr15 102531392 6676013 0.0651118927557328 0.3141371364274021 chr16 90354753 6847713 0.07578697049838651 0.374856643919237 chr17 81195210 6313911 0.0777621118290106 0.40963744344307407 chr18 78077248 6355731 0.08140311246625906 1.0355127229844692 chr19 59128983 4646618 0.0785844397154607 0.7100030285581519 chr20 63025520 5055058 0.08020652586444348 0.3738988278338504 chr21 48129895 3087585 0.06415108530779051 0.3757726034918854 chr22 51304566 2780435 0.054194689026313955 0.29235261716864197 chrMT 16571 25570 1.5430571480296904 1.511374873727624 chrX 155270560 13075512 0.08421114730313332 0.4503854907867203 chrY 59373566 672663 0.011329334673952378 0.3245045184347936