BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971307.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 5,268,394 number of mapped reads = 4,419,343 (83.88%) number of secondary alignments = 0 number of mapped bases = 174,538,896 bp number of sequenced bases = 174,522,309 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 183,115 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8202 >>>>>>> ACTG content number of A's = 51,651,024 bp (29.6%) number of C's = 34,612,615 bp (19.83%) number of T's = 52,919,676 bp (30.32%) number of G's = 35,328,636 bp (20.24%) number of N's = 10,358 bp (0.01%) GC percentage = 40.08% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 473,085 number of insertions = 5,691 mapped reads with insertion percentage = 0.13% number of deletions = 13,237 mapped reads with deletion percentage = 0.3% homopolymer indels = 40.88% >>>>>>> Coverage mean coverageData = 0.0564X std coverageData = 0.4473X There is a 4.9% of reference with a coverageData >= 1X There is a 0.55% 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 13706703 0.054991650351795915 0.8475792286276452 chr2 243199373 14344674 0.05898318660550165 0.3574499204895651 chr3 198022430 12257930 0.061901724971257045 0.2788697763087449 chr4 191154276 12263193 0.06415338048728766 0.29404014471606094 chr5 180915260 11258669 0.06223172661056895 0.280780595887827 chr6 171115067 10575449 0.061803143261487316 0.32557589649791724 chr7 159138663 9644928 0.06060706944609683 0.565775682244706 chr8 146364022 9157435 0.062566161238723 0.8067541919224903 chr9 141213431 7266898 0.05146038835356957 0.3587729879643631 chr10 135534747 8141033 0.06006602129858257 0.4338062400710199 chr11 135006516 7953066 0.05890875667067803 0.36148186458739967 chr12 133851895 7902952 0.059042511127690794 0.2776775439152271 chr13 115169878 5945942 0.05162757921823968 0.2510058869787563 chr14 107349540 5300744 0.04937835783926042 0.29593178532542985 chr15 102531392 4773319 0.046554707849865144 0.2381985461039799 chr16 90354753 4534165 0.05018180947271252 0.3077777176102318 chr17 81195210 3981237 0.04903290477356977 0.27722047059930394 chr18 78077248 4742390 0.060739717670376905 0.6079617937582056 chr19 59128983 2781259 0.04703715265997387 0.7473312414250745 chr20 63025520 3305186 0.05244202665840758 0.2609140566332395 chr21 48129895 2269515 0.047153957015696794 0.26786704744039347 chr22 51304566 1638615 0.03193897011037965 0.1998497459871626 chrMT 16571 6652 0.4014241747631404 0.7489749755088903 chrX 155270560 10144243 0.06533268766468028 0.3229201833980901 chrY 59373566 642699 0.010824665643293178 0.16592711995472373