BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081020.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 = 2,880,881 number of mapped reads = 2,311,151 (80.22%) number of supplementary alignments = 9,709 (0.34%) number of secondary alignments = 0 number of mapped bases = 142,482,603 bp number of sequenced bases = 142,433,795 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,810 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7643 >>>>>>> ACTG content number of A's = 40,508,297 bp (28.44%) number of C's = 28,999,523 bp (20.36%) number of T's = 40,991,850 bp (28.78%) number of G's = 31,932,284 bp (22.42%) number of N's = 1,841 bp (0%) GC percentage = 42.78% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,054,434 number of insertions = 9,861 mapped reads with insertion percentage = 0.42% number of deletions = 28,156 mapped reads with deletion percentage = 1.21% homopolymer indels = 45.22% >>>>>>> Coverage mean coverageData = 0.046X std coverageData = 0.3534X There is a 3.95% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 11368229 0.045609631600476534 0.4787621055484552 chr2 243199373 13240510 0.05444302687408655 0.39777802309281435 chr3 198022430 9235043 0.04663634821570466 0.2432384559469918 chr4 191154276 10185074 0.05328195744886188 0.2754833685433239 chr5 180915260 7071883 0.039089477581935324 0.22519402742898134 chr6 171115067 7957177 0.04650190739778631 0.3151629321312072 chr7 159138663 8070617 0.05071436976946325 0.6150895572803928 chr8 146364022 7488967 0.05116672046631788 0.3516372004936047 chr9 141213431 5724225 0.04053598131186261 0.3544450696389993 chr10 135534747 6460387 0.047665909613569424 0.30565981310634194 chr11 135006516 6363915 0.047137835924897134 0.35274542166597744 chr12 133851895 6204648 0.046354577198925724 0.24855172537026107 chr13 115169878 4741142 0.041166510569716847 0.2308228599605355 chr14 107349540 4564093 0.04251618591006538 0.2535419541026962 chr15 102531392 4255341 0.041502811158557175 0.24337418590256946 chr16 90354753 4176308 0.046221231992079045 0.274381367042054 chr17 81195210 4203419 0.05176929772088772 0.2937686364231066 chr18 78077248 3660214 0.046879393085166116 0.7080604663663033 chr19 59128983 2927092 0.04950350659675645 0.39761446433214126 chr20 63025520 2896200 0.04595281403469579 0.25130266849118416 chr21 48129895 2099999 0.043631904869104746 0.2578484664910517 chr22 51304566 1790544 0.03490028548336224 0.21037776519441842 chrMT 16571 18000 1.0862349888359182 1.2471950338062703 chrX 155270560 7412531 0.04773944912673723 0.28568983637639433 chrY 59373566 367045 0.006181959830406683 0.13183093223418835