BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818896.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,387,818 number of mapped reads = 1,325,693 (95.52%) number of supplementary alignments = 20,718 (1.49%) number of secondary alignments = 0 number of mapped bases = 122,545,695 bp number of sequenced bases = 122,465,689 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 232,045 duplication rate = 14.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1343 >>>>>>> ACTG content number of A's = 35,715,265 bp (29.16%) number of C's = 25,718,747 bp (21%) number of T's = 35,507,143 bp (28.99%) number of G's = 25,522,731 bp (20.84%) number of N's = 1,803 bp (0%) GC percentage = 41.84% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 760,573 number of insertions = 18,042 mapped reads with insertion percentage = 1.31% number of deletions = 40,693 mapped reads with deletion percentage = 3% homopolymer indels = 40.2% >>>>>>> Coverage mean coverageData = 0.0396X std coverageData = 0.5151X There is a 2.98% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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% 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 11574493 0.04643716815453792 0.7536898042926347 chr2 243199373 9399967 0.038651279746514805 0.7769350837111961 chr3 198022430 7582374 0.03829048052788767 0.24497202951864422 chr4 191154276 6285566 0.032882162677857124 0.3140469722865519 chr5 180915260 5431800 0.030024001292096644 0.22931850518487187 chr6 171115067 5970676 0.03489275435926399 0.255567146491492 chr7 159138663 10986654 0.06903824496753501 1.0866397546944164 chr8 146364022 10781927 0.07366514565990814 0.42364425763777525 chr9 141213431 4507008 0.031916284223701075 0.4228457544177856 chr10 135534747 5746510 0.04239879534360292 0.772031156634638 chr11 135006516 5358128 0.03968792143336252 0.2953329961143973 chr12 133851895 4778628 0.03570086176217378 0.24142585096755056 chr13 115169878 3789048 0.03289964412396095 0.22489953675027904 chr14 107349540 3568368 0.033240645465271675 0.24838627483424083 chr15 102531392 3355558 0.03272712809750988 0.23065456528010786 chr16 90354753 3051814 0.03377590994023303 0.5288187878749613 chr17 81195210 2946051 0.036283556628525254 0.30529593833973784 chr18 78077248 2387787 0.030582366325206545 0.4782476858390629 chr19 59128983 2049789 0.03466640040130574 0.590464687389343 chr20 63025520 4965194 0.07878069074241673 0.3745720238951766 chr21 48129895 1201499 0.0249636738247611 0.2435442330254962 chr22 51304566 1100306 0.02144655117051375 0.20318948952545937 chrMT 16571 207231 12.50564238730312 8.325686021679946 chrX 155270560 5047434 0.03250734717515027 0.2687441218248805 chrY 59373566 471885 0.007947728792304643 0.6239407386521738