BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085055.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,948,947 number of mapped reads = 1,576,950 (80.91%) number of supplementary alignments = 7,069 (0.36%) number of secondary alignments = 0 number of mapped bases = 95,012,802 bp number of sequenced bases = 94,981,831 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,509 duplication rate = 2.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3889 >>>>>>> ACTG content number of A's = 27,821,971 bp (29.29%) number of C's = 18,849,931 bp (19.85%) number of T's = 27,182,899 bp (28.62%) number of G's = 21,125,004 bp (22.24%) number of N's = 2,026 bp (0%) GC percentage = 42.09% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 840,038 number of insertions = 7,477 mapped reads with insertion percentage = 0.47% number of deletions = 19,387 mapped reads with deletion percentage = 1.22% homopolymer indels = 44.61% >>>>>>> Coverage mean coverageData = 0.0307X std coverageData = 0.2529X There is a 2.77% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 7788769 0.031248744611954246 0.3925724998628974 chr2 243199373 8161704 0.033559724679059925 0.2855504870360707 chr3 198022430 6247345 0.031548673551778955 0.19164802061941436 chr4 191154276 5912919 0.030932705894583284 0.20199373377246363 chr5 180915260 5989267 0.033105372095200813 0.19573956210314467 chr6 171115067 5457224 0.03189213022369328 0.23462545593040054 chr7 159138663 5171085 0.03249420915393766 0.2551855729787205 chr8 146364022 4866707 0.03325070555932113 0.3035759380530067 chr9 141213431 4037958 0.028594716319866202 0.24191137661609605 chr10 135534747 4583318 0.03381655333004754 0.28849849251129683 chr11 135006516 4134785 0.030626558795132524 0.23858981454216102 chr12 133851895 4348666 0.03248863977607489 0.19631514979257428 chr13 115169878 3071533 0.026669586295819468 0.17495973627707523 chr14 107349540 2713803 0.025280061749682392 0.18638110245947495 chr15 102531392 2520514 0.02458285165971413 0.16819524953504758 chr16 90354753 2758334 0.030527824031570314 0.20134785457851376 chr17 81195210 2604189 0.03207318510537752 0.214691462253288 chr18 78077248 2639857 0.033810835648305636 0.4399108655073153 chr19 59128983 1907381 0.03225797068080809 0.30548593117221057 chr20 63025520 1961111 0.03111614152489341 0.19518832641692016 chr21 48129895 1143372 0.023755962899981393 0.17964184977879702 chr22 51304566 1087910 0.021204935248843152 0.1564199076457107 chrMT 16571 7906 0.47709854565204274 0.8198424402423053 chrX 155270560 5653611 0.03641135190083684 0.22818218354043412 chrY 59373566 243534 0.004101724326276781 0.10034564304360608