BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10156414.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 = 4,996,868 number of mapped reads = 4,881,230 (97.69%) number of supplementary alignments = 660,740 (13.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,441,847 number of mapped paired reads (second in pair) = 2,439,383 number of mapped paired reads (both in pair) = 4,804,102 number of mapped paired reads (singletons) = 77,128 number of mapped bases = 557,731,044 bp number of sequenced bases = 557,269,288 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,038,972 duplication rate = 67.6% >>>>>>> Insert size mean insert size = 1,085,806.4655 std insert size = 9,724,046.465 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 52.3219 >>>>>>> ACTG content number of A's = 163,969,363 bp (29.42%) number of C's = 112,544,595 bp (20.2%) number of T's = 162,736,135 bp (29.2%) number of G's = 118,014,743 bp (21.18%) number of N's = 4,452 bp (0%) GC percentage = 41.37% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 5,148,235 number of insertions = 67,118 mapped reads with insertion percentage = 1.32% number of deletions = 201,293 mapped reads with deletion percentage = 4.01% homopolymer indels = 39.97% >>>>>>> Coverage mean coverageData = 0.1802X std coverageData = 3.5839X There is a 3.57% of reference with a coverageData >= 1X There is a 2.82% of reference with a coverageData >= 2X There is a 2.19% of reference with a coverageData >= 3X There is a 1.79% of reference with a coverageData >= 4X There is a 1.37% of reference with a coverageData >= 5X There is a 1.12% of reference with a coverageData >= 6X There is a 0.85% of reference with a coverageData >= 7X There is a 0.72% of reference with a coverageData >= 8X There is a 0.54% of reference with a coverageData >= 9X There is a 0.48% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.11% 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 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% 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 0.02% 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 0.01% 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 46246300 0.18554136320486841 1.9943477099413747 chr2 243199373 49921922 0.2052715900710813 11.481175516973407 chr3 198022430 37123935 0.18747338369698827 1.321371231073306 chr4 191154276 35658093 0.18654091211645196 1.9090251360969235 chr5 180915260 31818858 0.1758771371746087 1.27327911942014 chr6 171115067 32279495 0.1886420381672176 1.5197727240208643 chr7 159138663 30456189 0.19138145580624866 1.7714678323987205 chr8 146364022 26441356 0.18065475134319553 2.0367419240219613 chr9 141213431 24175017 0.17119488442993783 1.816668236942185 chr10 135534747 28123326 0.20749901130519688 2.2384587359625576 chr11 135006516 26097453 0.19330513647207961 1.4101836388082984 chr12 133851895 25457393 0.19019075523734646 1.3660254430484196 chr13 115169878 17796538 0.15452424113881583 1.1964512412596335 chr14 107349540 16939619 0.15779871064189002 1.2182849781041212 chr15 102531392 16865180 0.16448796481764336 1.2524930757930848 chr16 90354753 18550402 0.2053063218489458 1.6128406816894154 chr17 81195210 16419288 0.2022199092778995 1.5048709907838385 chr18 78077248 14880191 0.19058293396816445 2.3011559653591243 chr19 59128983 13050496 0.22071233662178832 1.7053236268308434 chr20 63025520 12953830 0.2055330919919423 1.4736735180202694 chr21 48129895 8118834 0.16868588639139978 1.6485075694072295 chr22 51304566 8344754 0.16265129306424694 1.3628645153303325 chrMT 16571 1015705 61.29412829642146 52.679741242923654 chrX 155270560 14305771 0.09213447159590331 0.9274502411611156 chrY 59373566 4691099 0.07900989137152382 1.394350645878866