BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472519.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,208,066 number of mapped reads = 14,998,638 (98.62%) number of supplementary alignments = 57,537 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,532,661 number of mapped paired reads (second in pair) = 7,465,977 number of mapped paired reads (both in pair) = 14,885,850 number of mapped paired reads (singletons) = 112,788 number of mapped bases = 1,478,434,193 bp number of sequenced bases = 1,478,251,799 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,120,955 duplication rate = 45.13% >>>>>>> Insert size mean insert size = 31,556.0917 std insert size = 1,798,961.0293 median insert size = 248 >>>>>>> Mapping quality mean mapping quality = 54.9895 >>>>>>> ACTG content number of A's = 414,496,679 bp (28.04%) number of C's = 326,341,129 bp (22.08%) number of T's = 413,036,012 bp (27.94%) number of G's = 324,151,363 bp (21.93%) number of N's = 226,616 bp (0.02%) GC percentage = 44% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 9,605,902 number of insertions = 82,553 mapped reads with insertion percentage = 0.54% number of deletions = 75,158 mapped reads with deletion percentage = 0.5% homopolymer indels = 44.03% >>>>>>> Coverage mean coverageData = 0.4776X std coverageData = 16.422X There is a 4.8% of reference with a coverageData >= 1X There is a 2.04% of reference with a coverageData >= 2X There is a 0.91% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 154936046 0.6216074623140057 19.450882091357297 chr2 243199373 134443994 0.5528139005522847 22.138154786760474 chr3 198022430 180859191 0.9133267933334622 23.66158778611362 chr4 191154276 51522773 0.2695350272991016 11.002620142007737 chr5 180915260 77861588 0.4303760113989279 12.84847210703428 chr6 171115067 82886627 0.4843911670268054 12.219810523939802 chr7 159138663 66509769 0.4179359543821227 16.890568136973975 chr8 146364022 63507969 0.4339042350175373 19.24793219981046 chr9 141213431 88413785 0.6261003955069968 16.86616374651355 chr10 135534747 37739639 0.27844991661068286 9.70809250386535 chr11 135006516 79435789 0.5883848524763057 20.172401808189647 chr12 133851895 65490416 0.4892752246802333 16.1337153955703 chr13 115169878 37303343 0.32389843288711306 11.012991436722672 chr14 107349540 51824744 0.48276633509561384 20.206651936970438 chr15 102531392 38780852 0.3782339363928659 13.46845955690457 chr16 90354753 39472563 0.4368620541743941 12.357648519333319 chr17 81195210 62316538 0.7674903236286968 17.39445175977432 chr18 78077248 22158925 0.2838077105381583 10.014468274076858 chr19 59128983 27593279 0.4666624995055301 16.82358552528614 chr20 63025520 20754159 0.3292977035334258 9.576662003440239 chr21 48129895 5065366 0.10524365365850061 3.2359992587643314 chr22 51304566 9671139 0.18850445007175384 6.346997767202903 chrMT 16571 3047 0.18387544505461348 0.6723995326316311 chrX 155270560 77483971 0.49902551391583827 16.375436663489662 chrY 59373566 2398681 0.0403998136140248 1.6887580787529164