BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080906.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 = 2,599,490 number of mapped reads = 2,281,331 (87.76%) number of supplementary alignments = 19,795 (0.76%) number of secondary alignments = 0 number of mapped bases = 155,417,460 bp number of sequenced bases = 155,361,548 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,471 duplication rate = 2.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6611 >>>>>>> ACTG content number of A's = 44,672,965 bp (28.75%) number of C's = 27,186,393 bp (17.5%) number of T's = 50,103,956 bp (32.25%) number of G's = 32,673,706 bp (21.03%) number of N's = 724,528 bp (0.47%) GC percentage = 38.53% >>>>>>> Mismatches and indels general error rate = 0.0116 number of mismatches = 1,781,693 number of insertions = 11,877 mapped reads with insertion percentage = 0.52% number of deletions = 33,987 mapped reads with deletion percentage = 1.47% homopolymer indels = 49.57% >>>>>>> Coverage mean coverageData = 0.0502X std coverageData = 0.398X There is a 4.09% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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 11751027 0.04714542717227573 0.5984957456103707 chr2 243199373 13201233 0.05428152563534775 0.37731319004007713 chr3 198022430 10631635 0.05368904421584969 0.2723903476346762 chr4 191154276 10820940 0.056608411940520756 0.2900875470700483 chr5 180915260 9800085 0.054169476914219396 0.27570098852951497 chr6 171115067 9432264 0.055122346415000384 0.35685532610053716 chr7 159138663 8524150 0.053564293172426614 0.5631007728815336 chr8 146364022 9990824 0.06826010834821142 0.7525559173056305 chr9 141213431 7690628 0.05446102361184044 0.3955748207822576 chr10 135534747 6950523 0.051282222115336965 0.3468384302043313 chr11 135006516 6853675 0.05076551268088423 0.32535186329927296 chr12 133851895 7004659 0.05233141450855067 0.2726753004301765 chr13 115169878 5107765 0.04434983425093148 0.24737055114883 chr14 107349540 4580033 0.04266467280623652 0.2567498599575386 chr15 102531392 4053569 0.039534906538672566 0.23379328398222404 chr16 90354753 3674256 0.040664778310002134 0.2580027050397043 chr17 81195210 3326894 0.04097401804860164 0.2581992367150505 chr18 78077248 4248327 0.05441184351169755 0.643938374401983 chr19 59128983 2194415 0.0371123413369041 0.43306485714198356 chr20 63025520 2751044 0.0436496834932897 0.2526635622797394 chr21 48129895 2016028 0.04188723037937232 0.25574489309469745 chr22 51304566 1277738 0.02490495680248031 0.18245630411060582 chrMT 16571 12298 0.7421398829280068 0.9516429656158253 chrX 155270560 9194884 0.05921846356450315 0.35363707232730246 chrY 59373566 328566 0.005533876809757392 0.12626072971259822