BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779226.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 8,764,110 number of mapped reads = 8,457,627 (96.5%) number of supplementary alignments = 19,907 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,262,236 number of mapped paired reads (second in pair) = 4,195,391 number of mapped paired reads (both in pair) = 8,377,994 number of mapped paired reads (singletons) = 79,633 number of mapped bases = 672,888,019 bp number of sequenced bases = 672,757,886 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 108,219 duplication rate = 1.15% >>>>>>> Insert size mean insert size = 44,590.7584 std insert size = 1,990,378.99 median insert size = 198 >>>>>>> Mapping quality mean mapping quality = 52.9998 >>>>>>> ACTG content number of A's = 205,754,272 bp (30.58%) number of C's = 129,724,483 bp (19.28%) number of T's = 205,219,946 bp (30.5%) number of G's = 131,929,516 bp (19.61%) number of N's = 129,669 bp (0.02%) GC percentage = 38.89% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 2,614,356 number of insertions = 49,993 mapped reads with insertion percentage = 0.59% number of deletions = 62,994 mapped reads with deletion percentage = 0.73% homopolymer indels = 46.62% >>>>>>> Coverage mean coverageData = 0.2174X std coverageData = 0.7647X There is a 14% of reference with a coverageData >= 1X There is a 4.55% of reference with a coverageData >= 2X There is a 1.66% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.32% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% 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 58600354 0.23510615044766528 1.0430078208549274 chr2 243199373 53832422 0.22135099007841602 0.6470239835154178 chr3 198022430 35880157 0.1811923881552206 0.5917941680320509 chr4 191154276 47699981 0.2495365628127513 0.7158588347179892 chr5 180915260 38647625 0.213622803294758 0.63795671802209 chr6 171115067 35660276 0.2083993924392409 0.6329594623272699 chr7 159138663 60566685 0.38059063623024153 1.3751752308779537 chr8 146364022 64878224 0.44326620103402187 0.9541468082128214 chr9 141213431 25076799 0.17758083506943473 0.6090360590048617 chr10 135534747 20529355 0.15146931288402377 1.0609991260254064 chr11 135006516 25698089 0.1903470273982924 0.6033312713037888 chr12 133851895 38372388 0.28667795850032607 0.7426158998099495 chr13 115169878 12026965 0.10442804324234849 0.41845343972622095 chr14 107349540 16862560 0.15708087803636606 0.5574290852803202 chr15 102531392 18824716 0.1835995360328279 0.6014371067670006 chr16 90354753 13248391 0.14662638721396318 0.5101135449145171 chr17 81195210 13424918 0.16534125596817842 0.5696557721895876 chr18 78077248 20704839 0.2651840264656869 0.7478074367879128 chr19 59128983 7713573 0.1304533345347746 0.7092120847394364 chr20 63025520 14101027 0.22373519488613502 0.6525772585133912 chr21 48129895 9197532 0.19109811064412255 0.5939230283328252 chr22 51304566 2922388 0.05696155776856197 0.3006640571406635 chrMT 16571 882 0.05322551445295999 0.33388014595406496 chrX 155270560 37902911 0.24410880594492607 0.7230927106950874 chrY 59373566 514962 0.00867325368329738 0.12660657750629056