BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926925.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 11,845,990 number of mapped reads = 11,565,116 (97.63%) number of supplementary alignments = 110,241 (0.93%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,803,525 number of mapped paired reads (second in pair) = 5,761,591 number of mapped paired reads (both in pair) = 11,433,550 number of mapped paired reads (singletons) = 131,566 number of mapped bases = 1,068,513,817 bp number of sequenced bases = 1,067,680,201 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 620,011 duplication rate = 4.22% >>>>>>> Insert size mean insert size = 95,858.5706 std insert size = 3,029,613.8502 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 53.43 >>>>>>> ACTG content number of A's = 306,120,115 bp (28.67%) number of C's = 207,463,763 bp (19.43%) number of T's = 311,231,930 bp (29.15%) number of G's = 242,650,806 bp (22.73%) number of N's = 213,587 bp (0.02%) GC percentage = 42.16% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 10,236,374 number of insertions = 176,569 mapped reads with insertion percentage = 1.5% number of deletions = 587,410 mapped reads with deletion percentage = 4.94% homopolymer indels = 52.89% >>>>>>> Coverage mean coverageData = 0.3452X std coverageData = 1.5225X There is a 19.77% of reference with a coverageData >= 1X There is a 7.9% of reference with a coverageData >= 2X There is a 3.29% of reference with a coverageData >= 3X There is a 1.5% of reference with a coverageData >= 4X There is a 0.72% of reference with a coverageData >= 5X There is a 0.36% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 88601583 0.3554718646016934 1.631153642274372 chr2 243199373 94518831 0.388647511027917 2.3205662492959775 chr3 198022430 71780754 0.3624879969405486 0.892572101960539 chr4 191154276 64724698 0.33859926837315424 1.398132145024683 chr5 180915260 66613723 0.36820400335494086 0.8959088912390958 chr6 171115067 63197268 0.36932614472809694 1.835607081137326 chr7 159138663 56173334 0.352983573828316 1.0511654923490499 chr8 146364022 52711508 0.360139788998146 1.001498444033332 chr9 141213431 46196124 0.327136899605534 1.7230735555425962 chr10 135534747 53318920 0.3933966837301139 3.301164053782011 chr11 135006516 50232375 0.3720737079090316 1.132057292026902 chr12 133851895 48163965 0.3598302810729725 0.9024606506928806 chr13 115169878 31621272 0.27456199962285277 0.7678817905980813 chr14 107349540 32135637 0.2993551439531087 0.8271157362421883 chr15 102531392 30932837 0.3016913785779871 0.8279533985002504 chr16 90354753 32370143 0.3582561174175309 2.0736016628568135 chr17 81195210 26432722 0.32554533697246424 1.0837615040035615 chr18 78077248 29468721 0.3774303238761694 1.8521054806862522 chr19 59128983 15237523 0.25769973077331637 1.163004664540514 chr20 63025520 24825403 0.39389445735632167 0.9904488990841911 chr21 48129895 14017622 0.29124563849557533 1.1664362311267014 chr22 51304566 12554219 0.24469983821712868 0.7686428696857615 chrMT 16571 282692 17.05944119244463 13.862655850652153 chrX 155270560 60679164 0.39079632352713867 0.992474102367448 chrY 59373566 1722779 0.02901592604358647 1.1397628407294662