BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472405.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 = 18,137,966 number of mapped reads = 18,004,500 (99.26%) number of supplementary alignments = 60,162 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,027,545 number of mapped paired reads (second in pair) = 8,976,955 number of mapped paired reads (both in pair) = 17,924,156 number of mapped paired reads (singletons) = 80,344 number of mapped bases = 1,766,916,394 bp number of sequenced bases = 1,766,717,697 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,449,238 duplication rate = 47.12% >>>>>>> Insert size mean insert size = 15,815.6926 std insert size = 1,263,885.2017 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 55.0337 >>>>>>> ACTG content number of A's = 470,304,933 bp (26.62%) number of C's = 414,493,987 bp (23.46%) number of T's = 471,624,978 bp (26.69%) number of G's = 410,077,945 bp (23.21%) number of N's = 215,854 bp (0.01%) GC percentage = 46.67% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 9,104,367 number of insertions = 95,179 mapped reads with insertion percentage = 0.52% number of deletions = 85,261 mapped reads with deletion percentage = 0.47% homopolymer indels = 46.23% >>>>>>> Coverage mean coverageData = 0.5708X std coverageData = 18.144X There is a 4.95% of reference with a coverageData >= 1X There is a 2.17% of reference with a coverageData >= 2X There is a 0.9% of reference with a coverageData >= 3X There is a 0.66% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 186994144 0.7502253886059526 20.279999105487857 chr2 243199373 108471355 0.4460182345947084 15.617208169932825 chr3 198022430 178049590 0.8991384965834426 24.252135240670437 chr4 191154276 60915405 0.31867142223907147 11.902463666007453 chr5 180915260 104874796 0.5796901599124363 20.62091693484593 chr6 171115067 125438015 0.7330623608966006 17.867290636630944 chr7 159138663 88721978 0.5575136571305742 21.301712673038473 chr8 146364022 101688627 0.6947651862149565 22.82010747700925 chr9 141213431 79902156 0.5658254702415665 15.630620312975196 chr10 135534747 43810240 0.3232399142634619 10.307099145534705 chr11 135006516 81411836 0.6030215311977979 20.895258695752876 chr12 133851895 91239742 0.681646994986511 18.94229706295098 chr13 115169878 40947687 0.35554163737153566 15.229916494305055 chr14 107349540 53137636 0.49499640147503193 15.14861014470904 chr15 102531392 41986714 0.40950106285497423 14.826568010834393 chr16 90354753 79747577 0.8826052238779293 21.10197384530915 chr17 81195210 96537398 1.1889543484153806 29.608351374095207 chr18 78077248 24637684 0.31555523063517815 9.211452760021388 chr19 59128983 39548746 0.6688555086428596 15.56169378147233 chr20 63025520 41274502 0.6548855447761478 24.11723458271236 chr21 48129895 9347679 0.19421773099650436 9.631565864801725 chr22 51304566 26464962 0.515840286028343 14.584572711807583 chrMT 16571 2658 0.16040070001810391 0.5291740137369105 chrX 155270560 61463179 0.3958456709372337 11.191039602301071 chrY 59373566 302088 0.005087920776057143 0.2924751842837409