BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472608.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 = 14,940,304 number of mapped reads = 14,830,522 (99.27%) number of supplementary alignments = 70,921 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,435,896 number of mapped paired reads (second in pair) = 7,394,626 number of mapped paired reads (both in pair) = 14,759,558 number of mapped paired reads (singletons) = 70,964 number of mapped bases = 1,457,166,662 bp number of sequenced bases = 1,456,961,129 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,904,298 duplication rate = 49.13% >>>>>>> Insert size mean insert size = 21,126.1256 std insert size = 1,470,302.3916 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 54.7621 >>>>>>> ACTG content number of A's = 391,664,822 bp (26.88%) number of C's = 338,632,784 bp (23.24%) number of T's = 392,166,092 bp (26.92%) number of G's = 334,225,666 bp (22.94%) number of N's = 271,765 bp (0.02%) GC percentage = 46.18% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 8,496,896 number of insertions = 82,228 mapped reads with insertion percentage = 0.55% number of deletions = 78,121 mapped reads with deletion percentage = 0.52% homopolymer indels = 44.93% >>>>>>> Coverage mean coverageData = 0.4707X std coverageData = 19.2138X There is a 3.07% of reference with a coverageData >= 1X There is a 1.42% of reference with a coverageData >= 2X There is a 0.67% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.3% 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 0.17% 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 0.16% 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 0.15% 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 0.14% 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 222061621 0.8909170220282019 26.54520739505212 chr2 243199373 145842253 0.5996818626666442 31.19560645381754 chr3 198022430 148218004 0.7484909866018713 25.75354610186092 chr4 191154276 24705985 0.12924631097449266 6.652504249195736 chr5 180915260 64490709 0.3564691502529969 12.198182180044425 chr6 171115067 122603933 0.7164999269175987 20.0210979600501 chr7 159138663 93356634 0.5866370386685981 26.328751380302975 chr8 146364022 70540872 0.4819549984763332 17.325067651046275 chr9 141213431 59568292 0.42183163158184295 14.006602856825587 chr10 135534747 36968923 0.2727634338668888 12.547100870872246 chr11 135006516 36493908 0.27031219737571777 11.076404240532183 chr12 133851895 41276984 0.30837803230204547 11.251171522392672 chr13 115169878 51449332 0.4467255926067752 17.73168428333496 chr14 107349540 19135038 0.17824983693455976 7.002950365017577 chr15 102531392 16407607 0.1600252047685064 7.9841579164235466 chr16 90354753 60010194 0.6641620059544626 25.223744074509625 chr17 81195210 56314314 0.6935669480995246 20.328778387645652 chr18 78077248 10592933 0.13567246888619844 4.8880867717755745 chr19 59128983 30585422 0.5172661603193818 14.856317232567957 chr20 63025520 56408693 0.895013527853479 27.318530684286987 chr21 48129895 11758498 0.2443075764033975 13.591525915819831 chr22 51304566 24724922 0.4819243963587958 24.645397683708115 chrMT 16571 2211 0.13342586446201196 0.4591840631408342 chrX 155270560 52401190 0.33748310046669505 10.499886411499888 chrY 59373566 1248190 0.021022655098735354 1.1395275320054934