BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926932.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 12,670,104 number of mapped reads = 12,256,780 (96.74%) number of supplementary alignments = 328,073 (2.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,154,403 number of mapped paired reads (second in pair) = 6,102,377 number of mapped paired reads (both in pair) = 12,048,308 number of mapped paired reads (singletons) = 208,472 number of mapped bases = 1,077,806,858 bp number of sequenced bases = 1,076,951,893 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 984,407 duplication rate = 6.81% >>>>>>> Insert size mean insert size = 280,872.3538 std insert size = 5,289,779.9129 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 52.677 >>>>>>> ACTG content number of A's = 303,163,788 bp (28.15%) number of C's = 205,044,547 bp (19.04%) number of T's = 315,515,601 bp (29.3%) number of G's = 253,178,175 bp (23.51%) number of N's = 49,782 bp (0%) GC percentage = 42.55% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 10,114,273 number of insertions = 186,658 mapped reads with insertion percentage = 1.5% number of deletions = 579,207 mapped reads with deletion percentage = 4.6% homopolymer indels = 52.05% >>>>>>> Coverage mean coverageData = 0.3482X std coverageData = 1.4435X There is a 19.67% of reference with a coverageData >= 1X There is a 7.93% of reference with a coverageData >= 2X There is a 3.31% of reference with a coverageData >= 3X There is a 1.6% of reference with a coverageData >= 4X There is a 0.82% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.26% of reference with a coverageData >= 7X There is a 0.16% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 87595149 0.3514340251132213 1.4090358691424478 chr2 243199373 93375739 0.38394728509435755 3.470808582931342 chr3 198022430 73416026 0.37074601094431575 0.9475945222736504 chr4 191154276 64812461 0.33905838967473584 1.0820086938461577 chr5 180915260 66373939 0.3668786093555624 0.931829085994107 chr6 171115067 61565232 0.3597884925001958 0.9994836765389628 chr7 159138663 55818321 0.3507527331683062 1.053823113808438 chr8 146364022 54758020 0.3741221322819347 0.987427112910847 chr9 141213431 46287258 0.3277822631474764 1.1561746509069848 chr10 135534747 52729621 0.3890487285891344 1.53043675810591 chr11 135006516 51699341 0.3829395982635386 1.07969318611581 chr12 133851895 49476488 0.36963606678859495 0.9805801577225314 chr13 115169878 32702572 0.2839507392722948 0.8226981242785585 chr14 107349540 33276791 0.3099854084144189 0.9297984525652345 chr15 102531392 32896826 0.32084638039440644 0.9055615004958296 chr16 90354753 32138384 0.3556911278369606 1.3195514115886984 chr17 81195210 27717588 0.34136974336293974 0.9577923138619305 chr18 78077248 28816330 0.36907461185107343 1.1992526252696305 chr19 59128983 17649005 0.29848314827265 1.0674637986413409 chr20 63025520 25273633 0.4010063383848321 1.0163055676479378 chr21 48129895 13313914 0.27662462176574454 1.0684846050546446 chr22 51304566 13244306 0.25815062932215427 0.8372890893127345 chrMT 16571 1278697 77.16474563997345 63.83112493841487 chrX 155270560 59967371 0.3862121125859274 0.9994773781702231 chrY 59373566 1623846 0.027349645800287623 0.74082938654918