BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818888.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 = 1,607,692 number of mapped reads = 1,586,111 (98.66%) number of supplementary alignments = 21,421 (1.33%) number of secondary alignments = 0 number of mapped bases = 147,189,775 bp number of sequenced bases = 147,097,273 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 278,064 duplication rate = 14.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2908 >>>>>>> ACTG content number of A's = 41,881,888 bp (28.47%) number of C's = 30,089,955 bp (20.46%) number of T's = 41,609,905 bp (28.29%) number of G's = 33,513,430 bp (22.78%) number of N's = 2,095 bp (0%) GC percentage = 43.24% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 914,434 number of insertions = 23,818 mapped reads with insertion percentage = 1.46% number of deletions = 46,941 mapped reads with deletion percentage = 2.89% homopolymer indels = 39.1% >>>>>>> Coverage mean coverageData = 0.0475X std coverageData = 0.5914X There is a 3.52% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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 12911579 0.051801592101148666 0.8958772651697262 chr2 243199373 11167188 0.04591783219770061 0.7947176280659485 chr3 198022430 9253903 0.046731589951703956 0.2716488101402335 chr4 191154276 7488702 0.03917622015423814 0.34785695370419173 chr5 180915260 6115479 0.0338030025770076 0.24930913380060601 chr6 171115067 7387643 0.04317353889123043 0.2899635845372965 chr7 159138663 13424219 0.08435548437402669 1.4020165275164334 chr8 146364022 12996258 0.08879407536368467 0.4988793895520986 chr9 141213431 5458375 0.03865337001832354 0.49070041861896735 chr10 135534747 6769464 0.04994633590159725 0.6806362542104235 chr11 135006516 6572406 0.04868213916430523 0.3606231487612738 chr12 133851895 5822926 0.04350275354712012 0.2687108925450833 chr13 115169878 4592795 0.03987843939541205 0.25056793911311687 chr14 107349540 4374999 0.04075470654089435 0.2815793934320916 chr15 102531392 4105905 0.040045345331896014 0.2581838010420216 chr16 90354753 3692360 0.04086514408378716 0.5779864326203191 chr17 81195210 3693405 0.04548796659310322 0.36288118257613816 chr18 78077248 2858556 0.03661189492744416 0.5689120003809642 chr19 59128983 2592913 0.04385181121752085 0.7835345159958589 chr20 63025520 6139234 0.09740870047561687 0.42829848089467243 chr21 48129895 1441188 0.029943717932482503 0.27399487446769366 chr22 51304566 1332539 0.02597310734487063 0.2227394878769159 chrMT 16571 303975 18.34379337396657 11.267244454879723 chrX 155270560 6145645 0.03958023336812851 0.31145616459860676 chrY 59373566 548119 0.009231700854888858 0.6647425638257064