BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708535.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 23,342,018 number of mapped reads = 22,806,735 (97.71%) number of supplementary alignments = 617 (0%) number of secondary alignments = 0 number of mapped bases = 1,137,715,851 bp number of sequenced bases = 1,137,613,188 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 255,197 duplication rate = 1.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.664 >>>>>>> ACTG content number of A's = 353,469,416 bp (31.07%) number of C's = 213,798,316 bp (18.79%) number of T's = 353,125,373 bp (31.04%) number of G's = 217,180,643 bp (19.09%) number of N's = 39,440 bp (0%) GC percentage = 37.88% >>>>>>> Mismatches and indels general error rate = 0.002 number of mismatches = 2,139,921 number of insertions = 67,512 mapped reads with insertion percentage = 0.3% number of deletions = 61,482 mapped reads with deletion percentage = 0.27% homopolymer indels = 49.27% >>>>>>> Coverage mean coverageData = 0.3675X std coverageData = 0.7071X There is a 27.02% of reference with a coverageData >= 1X There is a 7.2% of reference with a coverageData >= 2X There is a 1.86% of reference with a coverageData >= 3X There is a 0.48% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% 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 89204740 0.35789174623560915 0.7119647616552826 chr2 243199373 102683000 0.42221737142389754 0.747299844558253 chr3 198022430 85898110 0.43377969859273013 0.7488828831534039 chr4 191154276 94346067 0.4935598040192415 0.8004038072416797 chr5 180915260 79228040 0.4379290060993197 0.7539820530647603 chr6 171115067 76584085 0.4475589808815608 0.767388995437255 chr7 159138663 64653684 0.40627263533061103 0.7412444725089955 chr8 146364022 65319905 0.4462838893563611 0.7623683766728755 chr9 141213431 49694685 0.3519118871915236 0.7006155364054422 chr10 135534747 48626312 0.3587737689140335 0.6858582535536719 chr11 135006516 49514207 0.3667542017009016 0.7107705390702684 chr12 133851895 55149657 0.4120199941883527 0.748218123103459 chr13 115169878 45479921 0.39489423614740654 0.7307826632607641 chr14 107349540 37151147 0.3460764433643591 0.6971860318895754 chr15 102531392 30466928 0.2971473165993884 0.6507878465226499 chr16 90354753 21396920 0.2368101211012109 0.5640045783119242 chr17 81195210 18355360 0.22606456710931594 0.5570112943631601 chr18 78077248 32774014 0.41976394967199665 0.7419204528679514 chr19 59128983 8952185 0.1514009635511573 0.43898004611648433 chr20 63025520 17777403 0.2820667405838143 0.6237587846636427 chr21 48129895 14142686 0.29384410666177435 0.655140987415616 chr22 51304566 6016805 0.11727620890507094 0.39028102416095756 chrMT 16571 1299 0.07838995836099209 0.28064636595218817 chrX 155270560 38701046 0.24924909139247003 0.5566488549376494 chrY 59373566 5597645 0.09427840328808952 0.36008809777556644