BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174006.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 6,301,944 number of mapped reads = 6,158,444 (97.72%) number of supplementary alignments = 538,149 (8.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,081,758 number of mapped paired reads (second in pair) = 3,076,686 number of mapped paired reads (both in pair) = 6,067,494 number of mapped paired reads (singletons) = 90,950 number of mapped bases = 729,439,408 bp number of sequenced bases = 728,969,388 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,753,725 duplication rate = 66.37% >>>>>>> Insert size mean insert size = 696,889.6853 std insert size = 7,837,285.5117 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 53.0638 >>>>>>> ACTG content number of A's = 219,551,173 bp (30.12%) number of C's = 142,675,527 bp (19.57%) number of T's = 219,053,011 bp (30.05%) number of G's = 147,680,622 bp (20.26%) number of N's = 9,055 bp (0%) GC percentage = 39.83% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 7,420,567 number of insertions = 73,267 mapped reads with insertion percentage = 1.15% number of deletions = 199,100 mapped reads with deletion percentage = 3.16% homopolymer indels = 42.02% >>>>>>> Coverage mean coverageData = 0.2356X std coverageData = 3.2751X There is a 4.78% of reference with a coverageData >= 1X There is a 3.85% of reference with a coverageData >= 2X There is a 2.98% of reference with a coverageData >= 3X There is a 2.48% of reference with a coverageData >= 4X There is a 1.89% of reference with a coverageData >= 5X There is a 1.54% of reference with a coverageData >= 6X There is a 1.14% of reference with a coverageData >= 7X There is a 0.94% of reference with a coverageData >= 8X There is a 0.69% of reference with a coverageData >= 9X There is a 0.58% of reference with a coverageData >= 10X There is a 0.42% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.24% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% 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 56938986 0.22844069864925232 2.3493391012655085 chr2 243199373 65927191 0.27108289872112457 9.965414152628883 chr3 198022430 63655022 0.3214535949286149 1.6727096030081114 chr4 191154276 37597496 0.19668665952311734 1.4320705534535165 chr5 180915260 44909597 0.24823553856098154 1.4416100471668847 chr6 171115067 35784461 0.20912513215449344 1.6829417408951048 chr7 159138663 32180521 0.2022168616560515 1.7745608081004938 chr8 146364022 46424991 0.31718854378024675 2.1411552809256458 chr9 141213431 28667768 0.20301020800209862 1.6443920018723752 chr10 135534747 30512760 0.22512868969313088 2.7448480641593305 chr11 135006516 29109121 0.21561271161163806 1.3952035868562473 chr12 133851895 34178006 0.2553419658347011 1.4641045504771288 chr13 115169878 15507632 0.1346500688313658 1.0626920205819268 chr14 107349540 19356535 0.18031316203124859 1.224100987795724 chr15 102531392 24649267 0.24040702578191858 1.4208421201402461 chr16 90354753 29630775 0.3279381993330224 2.072291212619355 chr17 81195210 29315728 0.36105243154122024 1.9694671853534116 chr18 78077248 15373978 0.19690727316618536 2.290598078418979 chr19 59128983 10699750 0.18095609728312087 1.8180332876815328 chr20 63025520 33392088 0.5298185243057099 2.339975931049456 chr21 48129895 9490606 0.197187340633093 1.3284725722036426 chr22 51304566 5576431 0.10869268438992351 0.902671804798579 chrMT 16571 1297104 78.27554160883471 70.29474906331377 chrX 155270560 28061734 0.18072797573474328 1.2358210421326747 chrY 59373566 1201860 0.020242341516088152 0.7371281651654219