BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038452.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 13,852,774 number of mapped reads = 13,463,241 (97.19%) number of supplementary alignments = 219,429 (1.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,808,782 number of mapped paired reads (second in pair) = 6,654,459 number of mapped paired reads (both in pair) = 13,291,280 number of mapped paired reads (singletons) = 171,961 number of mapped bases = 1,929,778,305 bp number of sequenced bases = 1,928,299,016 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,117,737 duplication rate = 9.99% >>>>>>> Insert size mean insert size = 73,747.2515 std insert size = 2,560,790.7075 median insert size = 248 >>>>>>> Mapping quality mean mapping quality = 53.7428 >>>>>>> ACTG content number of A's = 574,219,895 bp (29.78%) number of C's = 383,731,535 bp (19.9%) number of T's = 574,358,638 bp (29.79%) number of G's = 395,949,766 bp (20.53%) number of N's = 39,182 bp (0%) GC percentage = 40.43% >>>>>>> Mismatches and indels general error rate = 0.0149 number of mismatches = 27,697,252 number of insertions = 386,780 mapped reads with insertion percentage = 2.67% number of deletions = 740,972 mapped reads with deletion percentage = 5.27% homopolymer indels = 46.9% >>>>>>> Coverage mean coverageData = 0.6234X std coverageData = 8.8835X There is a 24.93% of reference with a coverageData >= 1X There is a 13.81% of reference with a coverageData >= 2X There is a 7.35% of reference with a coverageData >= 3X There is a 4.42% of reference with a coverageData >= 4X There is a 2.6% of reference with a coverageData >= 5X There is a 1.62% of reference with a coverageData >= 6X There is a 1.02% of reference with a coverageData >= 7X There is a 0.66% of reference with a coverageData >= 8X There is a 0.44% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 114307309 0.4586039085535518 8.20602432853958 chr2 243199373 206549056 0.8492992948629025 13.686547204033712 chr3 198022430 125363025 0.6330748743968044 1.4688303414207309 chr4 191154276 116344475 0.6086417601246858 8.074904533879588 chr5 180915260 111440053 0.6159792877615741 1.610899492860479 chr6 171115067 140639909 0.8219025446777285 12.741779882290093 chr7 159138663 137343346 0.8630419749096422 8.615307653921311 chr8 146364022 85049674 0.5810831981646418 2.808015858928736 chr9 141213431 78144749 0.5533804288063789 14.923194624583711 chr10 135534747 77817627 0.5741525971933972 17.949557882857096 chr11 135006516 100852925 0.7470226474105887 6.635300019502267 chr12 133851895 65825424 0.49177805065815466 1.3434940272493878 chr13 115169878 131630785 1.1429271896945137 2.1822846445008826 chr14 107349540 35038231 0.326393862516784 1.2704541393458582 chr15 102531392 32296789 0.31499415320529345 0.9654087899191282 chr16 90354753 66111879 0.7316923217088536 13.685245346463608 chr17 81195210 40629507 0.5003929049509201 5.060118011520795 chr18 78077248 31375762 0.4018553778944668 12.38316267534395 chr19 59128983 23405691 0.39584125774664514 4.985542245627977 chr20 63025520 55575310 0.8817905826084418 2.9887442390398125 chr21 48129895 17638781 0.3664828481342002 4.011349686739161 chr22 51304566 10268946 0.2001565708595995 1.0339052911080417 chrMT 16571 1281155 77.31307706233783 50.60877406705768 chrX 155270560 97134315 0.6255810180629219 2.200629485138652 chrY 59373566 27713582 0.4667663384072299 13.540588404792102