BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716459.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,484,022 number of mapped reads = 2,272,005 (91.46%) number of supplementary alignments = 14,577 (0.59%) number of secondary alignments = 0 number of mapped bases = 132,909,039 bp number of sequenced bases = 132,872,348 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 136,325 duplication rate = 4.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7158 >>>>>>> ACTG content number of A's = 35,025,342 bp (26.36%) number of C's = 25,647,761 bp (19.3%) number of T's = 39,722,974 bp (29.9%) number of G's = 32,475,325 bp (24.44%) number of N's = 946 bp (0%) GC percentage = 43.74% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 657,727 number of insertions = 10,117 mapped reads with insertion percentage = 0.44% number of deletions = 23,128 mapped reads with deletion percentage = 1.01% homopolymer indels = 40.86% >>>>>>> Coverage mean coverageData = 0.0429X std coverageData = 0.3576X There is a 3.57% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.1% 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 15604208 0.06260448996032793 0.5714977377158075 chr2 243199373 13562565 0.05576726959736035 0.5285781690751787 chr3 198022430 8397391 0.04240626175529712 0.23947476597239772 chr4 191154276 5515110 0.028851617214150103 0.23383242014466116 chr5 180915260 9316409 0.05149598215208601 0.26523037096261864 chr6 171115067 5003018 0.029237740940720316 0.229054019119568 chr7 159138663 8962575 0.05631928050067883 0.5839629208654761 chr8 146364022 5870506 0.040108941526627355 0.31714919805387526 chr9 141213431 3640036 0.025776839881469914 0.265499098761055 chr10 135534747 5944100 0.04385665028024142 0.31709420318496073 chr11 135006516 5743995 0.04254605755473313 0.3170301646552591 chr12 133851895 5276481 0.03942029360137187 0.2355826727482724 chr13 115169878 3838905 0.03333254377503118 0.21351049690643292 chr14 107349540 2735069 0.02547816227251649 0.1996486569602412 chr15 102531392 5770251 0.05627789584676662 0.27970551229416146 chr16 90354753 4011079 0.044392562281698675 0.2628328625270889 chr17 81195210 5155731 0.06349796989255893 0.3273503576950128 chr18 78077248 4268498 0.054670190219819226 0.5724535949914827 chr19 59128983 2236847 0.03782995895599963 0.4287462885943209 chr20 63025520 3489653 0.05536888866605147 0.28065837878672656 chr21 48129895 1665365 0.034601467549430553 0.23136904159492136 chr22 51304566 1658406 0.03232472524960059 0.209771287771869 chrMT 16571 4456 0.2689035061251584 0.5818325495592771 chrX 155270560 4928880 0.03174381544060896 0.24110984260909252 chrY 59373566 309505 0.005212841687831248 0.1374462761885039