BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818903.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 = 2,019,650 number of mapped reads = 1,985,242 (98.3%) number of supplementary alignments = 27,802 (1.38%) number of secondary alignments = 0 number of mapped bases = 184,115,556 bp number of sequenced bases = 184,000,518 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 405,153 duplication rate = 17.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2215 >>>>>>> ACTG content number of A's = 51,135,964 bp (27.79%) number of C's = 38,521,865 bp (20.94%) number of T's = 52,891,285 bp (28.75%) number of G's = 41,448,855 bp (22.53%) number of N's = 2,549 bp (0%) GC percentage = 43.46% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,132,849 number of insertions = 25,628 mapped reads with insertion percentage = 1.25% number of deletions = 58,679 mapped reads with deletion percentage = 2.89% homopolymer indels = 41.85% >>>>>>> Coverage mean coverageData = 0.0595X std coverageData = 0.7431X There is a 4.17% of reference with a coverageData >= 1X There is a 1.06% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 17469511 0.07008813430398635 1.167529490494941 chr2 243199373 13950428 0.05736210512351938 0.997269350897853 chr3 198022430 11362737 0.057381060317258 0.31688949067709543 chr4 191154276 9157659 0.04790716269407439 0.4188615039272513 chr5 180915260 8124553 0.044908058059889476 0.2954007650110258 chr6 171115067 9123109 0.053315638183982945 0.34646208742559914 chr7 159138663 16497276 0.103666046258036 1.6801729669174825 chr8 146364022 15945125 0.10894156078875723 0.6013603813471309 chr9 141213431 6827120 0.048346109514186365 0.6385065130404209 chr10 135534747 8605073 0.06348979276878718 1.0360322220864362 chr11 135006516 8135346 0.060258913725319746 0.4282726634716164 chr12 133851895 7208432 0.05385379116223943 0.3127105167698222 chr13 115169878 5610628 0.048716106133237375 0.2892796418722202 chr14 107349540 5401731 0.050319088465586345 0.3335121727865391 chr15 102531392 5062461 0.0493747417376329 0.2917256824923748 chr16 90354753 4588210 0.05077995177519881 0.6926862698528486 chr17 81195210 4655046 0.057331534705064496 0.46912815248176837 chr18 78077248 3567649 0.04569383644259593 0.7223812876393936 chr19 59128983 3321761 0.056178219740393644 1.0632194288126724 chr20 63025520 7570468 0.1201175016088721 0.5001460812088732 chr21 48129895 1770598 0.03678790489777715 0.3196425275597745 chr22 51304566 1735285 0.03382320786029064 0.27152362293535853 chrMT 16571 302300 18.242713173616558 13.04768244513349 chrX 155270560 7442886 0.047934946586139705 0.3736188644557871 chrY 59373566 680164 0.011455670356737542 0.8208634119387039