BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063552.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,975,263 number of mapped reads = 242,596 (12.28%) number of supplementary alignments = 1,614 (0.08%) number of secondary alignments = 0 number of mapped bases = 16,012,743 bp number of sequenced bases = 16,003,894 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,113 duplication rate = 5.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4288 >>>>>>> ACTG content number of A's = 4,418,963 bp (27.61%) number of C's = 2,946,909 bp (18.41%) number of T's = 5,132,016 bp (32.07%) number of G's = 3,505,637 bp (21.9%) number of N's = 369 bp (0%) GC percentage = 40.32% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 140,011 number of insertions = 1,278 mapped reads with insertion percentage = 0.52% number of deletions = 5,170 mapped reads with deletion percentage = 2.1% homopolymer indels = 48.46% >>>>>>> Coverage mean coverageData = 0.0052X std coverageData = 0.0975X There is a 0.39% of reference with a coverageData >= 1X There is a 0.09% 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 1429613 0.005735644686718755 0.12002730115212092 chr2 243199373 2088847 0.008589031189648667 0.12777835572883706 chr3 198022430 994274 0.005021017063572041 0.09063529841679423 chr4 191154276 1036420 0.00542190330076634 0.09597942815732358 chr5 180915260 648874 0.0035866183980278942 0.07609022171073933 chr6 171115067 646594 0.003778708744566602 0.07823322370935175 chr7 159138663 956281 0.006009105405139667 0.11231257831638172 chr8 146364022 910606 0.006221515284678362 0.11381693798381853 chr9 141213431 536672 0.0038004317025623433 0.0805948800846376 chr10 135534747 759087 0.005600681867949331 0.09814023331728801 chr11 135006516 681718 0.005049519239501003 0.09368991808862856 chr12 133851895 902683 0.006743894062911848 0.10617761125031892 chr13 115169878 313558 0.002722569524646019 0.066140708810253 chr14 107349540 531965 0.00495544741039412 0.09291226017224409 chr15 102531392 499809 0.004874692425906009 0.09156313903941685 chr16 90354753 499311 0.0055261177018546 0.095952899271172 chr17 81195210 300316 0.0036986910927381063 0.07577684889205367 chr18 78077248 353433 0.004526709240571594 0.09960273086979586 chr19 59128983 257167 0.0043492545779114785 0.0872648223528968 chr20 63025520 300730 0.004771559203319544 0.08864342112128676 chr21 48129895 299402 0.006220707524917725 0.10196615317828657 chr22 51304566 123603 0.002409200771720786 0.06144338025248115 chrMT 16571 10716 0.6466718966869833 1.1109865303240947 chrX 155270560 896663 0.005774842313958293 0.09685766205219395 chrY 59373566 34401 5.793992565647817E-4 0.028049952552052594