BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173902.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 = 17,475,214 number of mapped reads = 16,978,682 (97.16%) number of supplementary alignments = 1,909,695 (10.93%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,499,853 number of mapped paired reads (second in pair) = 8,478,829 number of mapped paired reads (both in pair) = 16,638,896 number of mapped paired reads (singletons) = 339,786 number of mapped bases = 2,001,924,892 bp number of sequenced bases = 2,000,701,887 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,742,031 duplication rate = 65.58% >>>>>>> Insert size mean insert size = 1,037,351.2026 std insert size = 9,110,984.4384 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 52.4599 >>>>>>> ACTG content number of A's = 599,285,332 bp (29.95%) number of C's = 393,080,784 bp (19.65%) number of T's = 598,983,327 bp (29.94%) number of G's = 409,328,941 bp (20.46%) number of N's = 23,503 bp (0%) GC percentage = 40.11% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 21,310,131 number of insertions = 218,603 mapped reads with insertion percentage = 1.24% number of deletions = 502,917 mapped reads with deletion percentage = 2.89% homopolymer indels = 42.55% >>>>>>> Coverage mean coverageData = 0.6467X std coverageData = 9.0127X There is a 11.7% of reference with a coverageData >= 1X There is a 9.48% of reference with a coverageData >= 2X There is a 7.64% of reference with a coverageData >= 3X There is a 6.44% of reference with a coverageData >= 4X There is a 5.14% of reference with a coverageData >= 5X There is a 4.26% of reference with a coverageData >= 6X There is a 3.33% of reference with a coverageData >= 7X There is a 2.75% of reference with a coverageData >= 8X There is a 2.13% of reference with a coverageData >= 9X There is a 1.78% of reference with a coverageData >= 10X There is a 1.39% of reference with a coverageData >= 11X There is a 1.18% of reference with a coverageData >= 12X There is a 0.93% of reference with a coverageData >= 13X There is a 0.8% of reference with a coverageData >= 14X There is a 0.63% of reference with a coverageData >= 15X There is a 0.55% of reference with a coverageData >= 16X There is a 0.44% of reference with a coverageData >= 17X There is a 0.38% of reference with a coverageData >= 18X There is a 0.3% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.19% of reference with a coverageData >= 22X There is a 0.16% of reference with a coverageData >= 23X There is a 0.14% of reference with a coverageData >= 24X There is a 0.11% of reference with a coverageData >= 25X There is a 0.1% of reference with a coverageData >= 26X There is a 0.09% of reference with a coverageData >= 27X There is a 0.08% of reference with a coverageData >= 28X There is a 0.07% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 163981324 0.6578973538445065 6.3731279196854835 chr2 243199373 167593908 0.6891214641412747 28.062882863125786 chr3 198022430 147068649 0.7426868208818567 2.6910193832419362 chr4 191154276 100738842 0.527002817347387 3.6595227909435613 chr5 180915260 116043380 0.6414239462165878 2.4160552364926096 chr6 171115067 104808954 0.6125057006230784 3.3771471137025784 chr7 159138663 123901655 0.7785766994913109 5.933137619500411 chr8 146364022 132617415 0.9060793300692433 5.181762812968129 chr9 141213431 80887277 0.572801584291228 4.616788413659568 chr10 135534747 106038666 0.7823725527742343 9.951757861329158 chr11 135006516 73032148 0.5409527640873275 2.4879378582212404 chr12 133851895 86741606 0.6480416732239764 2.498959903380692 chr13 115169878 51127103 0.44392773429872 2.0406021279568254 chr14 107349540 64679751 0.6025153996933755 2.4448722788302097 chr15 102531392 65661100 0.6403999664805097 2.47096652670986 chr16 90354753 63001904 0.6972727156921119 4.6749423727230175 chr17 81195210 79093480 0.9741150986616083 4.044246868293025 chr18 78077248 35248045 0.45145091435599777 7.433376320694139 chr19 59128983 33002723 0.55814798979377 4.816878826725165 chr20 63025520 88114031 1.3980690837616254 4.414801014064661 chr21 48129895 25066015 0.5207992870127808 2.6263124273418037 chr22 51304566 17417687 0.3394958452625835 1.7095570659777284 chrMT 16571 4246242 256.2453684147004 179.5407431964113 chrX 155270560 68038128 0.43819078130458217 2.0910797693850656 chrY 59373566 3774859 0.06357810814327709 2.3343484187329566