BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174012.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 = 6,522,478 number of mapped reads = 6,379,593 (97.81%) number of supplementary alignments = 601,776 (9.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,190,416 number of mapped paired reads (second in pair) = 3,189,177 number of mapped paired reads (both in pair) = 6,284,596 number of mapped paired reads (singletons) = 94,997 number of mapped bases = 754,449,478 bp number of sequenced bases = 754,019,077 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,100,260 duplication rate = 67.33% >>>>>>> Insert size mean insert size = 841,280.8999 std insert size = 8,272,292.8385 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 52.8304 >>>>>>> ACTG content number of A's = 228,354,084 bp (30.28%) number of C's = 146,715,549 bp (19.46%) number of T's = 227,508,521 bp (30.17%) number of G's = 151,431,772 bp (20.08%) number of N's = 9,151 bp (0%) GC percentage = 39.54% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 7,266,493 number of insertions = 77,411 mapped reads with insertion percentage = 1.17% number of deletions = 168,836 mapped reads with deletion percentage = 2.58% homopolymer indels = 43.1% >>>>>>> Coverage mean coverageData = 0.2437X std coverageData = 3.5959X There is a 4.56% of reference with a coverageData >= 1X There is a 3.71% of reference with a coverageData >= 2X There is a 2.94% of reference with a coverageData >= 3X There is a 2.48% of reference with a coverageData >= 4X There is a 1.95% of reference with a coverageData >= 5X There is a 1.63% of reference with a coverageData >= 6X There is a 1.25% of reference with a coverageData >= 7X There is a 1.03% of reference with a coverageData >= 8X There is a 0.78% of reference with a coverageData >= 9X There is a 0.66% of reference with a coverageData >= 10X There is a 0.5% of reference with a coverageData >= 11X There is a 0.43% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.22% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.15% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% 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 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 68464086 0.2746797007980173 1.9520397328008372 chr2 243199373 57706902 0.23728228115127584 10.567811835859976 chr3 198022430 42734660 0.21580716891515775 1.408888532700536 chr4 191154276 48670907 0.2546158423366893 1.9024587308868584 chr5 180915260 38491621 0.212760499031425 1.3889987696251862 chr6 171115067 36887401 0.21557073638641067 1.4538869812750073 chr7 159138663 67726376 0.4255809036173692 4.048991461192861 chr8 146364022 74989399 0.5123485811287695 2.6636600942498694 chr9 141213431 26263743 0.18598615453228384 1.687538061676873 chr10 135534747 34954040 0.2578972608404249 4.57968173744587 chr11 135006516 31032847 0.2298618460756368 1.495779521809147 chr12 133851895 28253326 0.21107901386080488 1.3864179908290113 chr13 115169878 19295697 0.1675411777374636 1.2516860096606672 chr14 107349540 25839921 0.24070826013786364 1.5022488795172488 chr15 102531392 17420052 0.1698996927692155 1.2306807092950445 chr16 90354753 17129210 0.18957729871720197 1.8951987753675539 chr17 81195210 18534951 0.22827640940888017 1.5926118809070742 chr18 78077248 12845566 0.1645238059620134 2.103914526581229 chr19 59128983 9422288 0.1593514300761777 1.5560570870901311 chr20 63025520 29429672 0.4669484995919113 2.1005248207912945 chr21 48129895 8782835 0.18248190651569052 1.393426436012975 chr22 51304566 7562658 0.1474071138229685 1.1130621844969517 chrMT 16571 1736563 104.7953050509927 82.92080870568482 chrX 155270560 28937612 0.18636895493904318 1.317502220762735 chrY 59373566 1337145 0.022520880756934827 0.8963232865738869