BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472728.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 14,925,114 number of mapped reads = 14,799,999 (99.16%) number of supplementary alignments = 51,201 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,422,499 number of mapped paired reads (second in pair) = 7,377,500 number of mapped paired reads (both in pair) = 14,724,282 number of mapped paired reads (singletons) = 75,717 number of mapped bases = 1,460,737,466 bp number of sequenced bases = 1,460,529,198 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,171,119 duplication rate = 47.26% >>>>>>> Insert size mean insert size = 23,005.9888 std insert size = 1,472,638.4329 median insert size = 242 >>>>>>> Mapping quality mean mapping quality = 55.3214 >>>>>>> ACTG content number of A's = 398,882,949 bp (27.31%) number of C's = 333,370,289 bp (22.83%) number of T's = 396,966,632 bp (27.18%) number of G's = 331,025,687 bp (22.66%) number of N's = 283,641 bp (0.02%) GC percentage = 45.49% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 8,903,281 number of insertions = 80,263 mapped reads with insertion percentage = 0.54% number of deletions = 82,037 mapped reads with deletion percentage = 0.54% homopolymer indels = 44.9% >>>>>>> Coverage mean coverageData = 0.4719X std coverageData = 16.1586X There is a 4.1% of reference with a coverageData >= 1X There is a 1.75% of reference with a coverageData >= 2X There is a 0.81% of reference with a coverageData >= 3X There is a 0.6% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 182638079 0.7327487420783597 27.076057216491705 chr2 243199373 87792524 0.3609899273876829 10.82706789906648 chr3 198022430 154431702 0.7798697450586785 18.227452722907035 chr4 191154276 56359318 0.2948368154735916 11.234975697507862 chr5 180915260 83495531 0.46151734795616467 16.165721966224364 chr6 171115067 103476948 0.6047214299369675 18.57695290405655 chr7 159138663 73299399 0.46060082206421454 18.044809393619396 chr8 146364022 56248001 0.384302099869871 12.141039802767494 chr9 141213431 102460026 0.7255685615343487 20.966097358946694 chr10 135534747 46499246 0.343079889321666 14.18817230868921 chr11 135006516 59850739 0.4433174099537536 14.613255021597226 chr12 133851895 77272839 0.5773010460554182 15.557435518806606 chr13 115169878 21801735 0.1893006693989899 6.748723807567361 chr14 107349540 36235115 0.3375432721928757 10.44914032957332 chr15 102531392 44036024 0.4294882098157801 24.117065267118704 chr16 90354753 43714977 0.4838149134224295 12.382308071488916 chr17 81195210 54392564 0.6698986799837084 14.718665138237139 chr18 78077248 23674460 0.30321842286244516 10.984466010926202 chr19 59128983 24289981 0.4107965293433171 9.523148559491661 chr20 63025520 34041505 0.5401225567040145 15.546013547059724 chr21 48129895 11435198 0.2375903375646259 11.794333999217368 chr22 51304566 13090573 0.25515415138683756 8.16975506636103 chrMT 16571 843 0.050872005310482166 0.22113296460726284 chrX 155270560 65489872 0.42177906745489935 13.162892932823508 chrY 59373566 4710267 0.07933272864223787 5.25743280265096