BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472530.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 = 17,225,174 number of mapped reads = 17,060,387 (99.04%) number of supplementary alignments = 63,550 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,549,831 number of mapped paired reads (second in pair) = 8,510,556 number of mapped paired reads (both in pair) = 16,977,148 number of mapped paired reads (singletons) = 83,239 number of mapped bases = 1,676,328,987 bp number of sequenced bases = 1,676,124,694 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,022,638 duplication rate = 45.35% >>>>>>> Insert size mean insert size = 27,194.7284 std insert size = 1,617,429.9494 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 54.9803 >>>>>>> ACTG content number of A's = 454,505,620 bp (27.12%) number of C's = 385,730,385 bp (23.01%) number of T's = 451,779,420 bp (26.95%) number of G's = 383,846,508 bp (22.9%) number of N's = 262,761 bp (0.02%) GC percentage = 45.91% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 9,150,553 number of insertions = 81,939 mapped reads with insertion percentage = 0.47% number of deletions = 76,769 mapped reads with deletion percentage = 0.44% homopolymer indels = 43.28% >>>>>>> Coverage mean coverageData = 0.5415X std coverageData = 21.1661X There is a 5.35% of reference with a coverageData >= 1X There is a 2.53% of reference with a coverageData >= 2X There is a 1.08% of reference with a coverageData >= 3X There is a 0.75% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 165273173 0.6630802857658677 21.622297834468377 chr2 243199373 124832693 0.5132936465259719 17.68776889029971 chr3 198022430 160826959 0.8121653642973677 21.14004718315758 chr4 191154276 75105002 0.39290254746904013 16.16661604470296 chr5 180915260 89766058 0.49617737055459005 21.76268327519461 chr6 171115067 85837053 0.5016335177544593 14.350665144445836 chr7 159138663 84555244 0.5313306169978317 26.300280898671847 chr8 146364022 60413272 0.412760398180367 14.362310774376793 chr9 141213431 91560100 0.6483809603068139 19.904189028119973 chr10 135534747 67097386 0.4950567104389843 29.221837460138484 chr11 135006516 114120537 0.8452965114661577 33.143360389608645 chr12 133851895 111726032 0.8346989185323077 27.150350093148 chr13 115169878 40795345 0.3542188783077464 14.871852600757615 chr14 107349540 46207159 0.4304364881302705 16.33040290237296 chr15 102531392 44390235 0.43294286885327765 19.213949643048974 chr16 90354753 41620956 0.4606393644836813 15.132021105413875 chr17 81195210 51650497 0.6361273897807519 16.944941026643406 chr18 78077248 26844846 0.34382418294251355 18.557583432054436 chr19 59128983 35338774 0.5976557046482602 17.297338525261537 chr20 63025520 53694752 0.8519525423986982 42.08859957194772 chr21 48129895 6884048 0.14303060499093131 4.762290778903476 chr22 51304566 15241932 0.29708724170866196 13.185775897183868 chrMT 16571 1061 0.0640275179530505 0.31277072550119217 chrX 155270560 79510166 0.51207496128049 21.75859038411748 chrY 59373566 3035707 0.05112893168653539 1.6632851308578886