BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2976569.sorted.bam outfile = /home/yangyx/scDNA/SRP067062/SRP067062.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 = 353,288,550 number of mapped reads = 351,000,799 (99.35%) number of supplementary alignments = 5,765,816 (1.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 176,309,201 number of mapped paired reads (second in pair) = 174,691,598 number of mapped paired reads (both in pair) = 349,127,168 number of mapped paired reads (singletons) = 1,873,631 number of mapped bases = 80,392,635,387 bp number of sequenced bases = 80,366,894,038 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,075,128 duplication rate = 12.44% >>>>>>> Insert size mean insert size = 46,158.3304 std insert size = 2,071,902.3869 median insert size = 530 >>>>>>> Mapping quality mean mapping quality = 55.6 >>>>>>> ACTG content number of A's = 23,811,744,947 bp (29.63%) number of C's = 16,395,465,087 bp (20.4%) number of T's = 23,615,662,244 bp (29.38%) number of G's = 16,538,335,849 bp (20.58%) number of N's = 5,685,911 bp (0.01%) GC percentage = 40.98% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 645,594,109 number of insertions = 7,291,500 mapped reads with insertion percentage = 1.98% number of deletions = 9,231,796 mapped reads with deletion percentage = 2.5% homopolymer indels = 46.38% >>>>>>> Coverage mean coverageData = 25.9692X std coverageData = 37.6088X There is a 90.09% of reference with a coverageData >= 1X There is a 88.45% of reference with a coverageData >= 2X There is a 86.77% of reference with a coverageData >= 3X There is a 85% of reference with a coverageData >= 4X There is a 83.15% of reference with a coverageData >= 5X There is a 81.22% of reference with a coverageData >= 6X There is a 79.21% of reference with a coverageData >= 7X There is a 77.13% of reference with a coverageData >= 8X There is a 75% of reference with a coverageData >= 9X There is a 72.83% of reference with a coverageData >= 10X There is a 70.64% of reference with a coverageData >= 11X There is a 68.42% of reference with a coverageData >= 12X There is a 66.19% of reference with a coverageData >= 13X There is a 63.97% of reference with a coverageData >= 14X There is a 61.75% of reference with a coverageData >= 15X There is a 59.55% of reference with a coverageData >= 16X There is a 57.37% of reference with a coverageData >= 17X There is a 55.23% of reference with a coverageData >= 18X There is a 53.12% of reference with a coverageData >= 19X There is a 51.05% of reference with a coverageData >= 20X There is a 49.03% of reference with a coverageData >= 21X There is a 47.05% of reference with a coverageData >= 22X There is a 45.13% of reference with a coverageData >= 23X There is a 43.26% of reference with a coverageData >= 24X There is a 41.45% of reference with a coverageData >= 25X There is a 39.7% of reference with a coverageData >= 26X There is a 38% of reference with a coverageData >= 27X There is a 36.37% of reference with a coverageData >= 28X There is a 34.79% of reference with a coverageData >= 29X There is a 33.28% of reference with a coverageData >= 30X There is a 31.82% of reference with a coverageData >= 31X There is a 30.42% of reference with a coverageData >= 32X There is a 29.07% of reference with a coverageData >= 33X There is a 27.78% of reference with a coverageData >= 34X There is a 26.54% of reference with a coverageData >= 35X There is a 25.35% of reference with a coverageData >= 36X There is a 24.21% of reference with a coverageData >= 37X There is a 23.12% of reference with a coverageData >= 38X There is a 22.08% of reference with a coverageData >= 39X There is a 21.09% of reference with a coverageData >= 40X There is a 20.14% of reference with a coverageData >= 41X There is a 19.23% of reference with a coverageData >= 42X There is a 18.37% of reference with a coverageData >= 43X There is a 17.54% of reference with a coverageData >= 44X There is a 16.75% of reference with a coverageData >= 45X There is a 16% of reference with a coverageData >= 46X There is a 15.28% of reference with a coverageData >= 47X There is a 14.59% of reference with a coverageData >= 48X There is a 13.94% of reference with a coverageData >= 49X There is a 13.32% of reference with a coverageData >= 50X There is a 12.72% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6634258543 26.61681851135689 64.26618677153297 chr2 243199373 7709355459 31.699734106633574 29.000598808193402 chr3 198022430 5109311481 25.80168055204655 23.203324184831537 chr4 191154276 5249238807 27.460744885455767 22.567725395376158 chr5 180915260 5427101012 29.99802787227567 24.78145707323274 chr6 171115067 4997252143 29.20404515284443 33.86627889405673 chr7 159138663 4536632700 28.507419972480225 28.280339077354416 chr8 146364022 4172540178 28.507963370943713 27.060239551799214 chr9 141213431 3225669966 22.842515355355964 61.687235643097814 chr10 135534747 3733043738 27.543075267628602 49.47907647467983 chr11 135006516 4078736653 30.211405892438556 35.98716792689846 chr12 133851895 4177505311 31.20990786869323 28.452732837659422 chr13 115169878 2600616760 22.580702568774104 21.503254609990012 chr14 107349540 2551761752 23.770588602429036 24.681515082786195 chr15 102531392 2595433898 25.313553706556526 27.23591225371524 chr16 90354753 2206973161 24.425645444462674 27.733810968623793 chr17 81195210 2196571411 27.05296791522554 54.97947281988122 chr18 78077248 1970623728 25.239410692344073 62.633794601260476 chr19 59128983 1379267928 23.326427379953415 46.74649134417929 chr20 63025520 1472012328 23.35581408927685 28.17235740639474 chr21 48129895 978543816 20.33131001012988 30.26003658819571 chr22 51304566 1040876041 20.288175539775544 30.414767407647588 chrMT 16571 1003724 60.57111821857462 23.51480423404609 chrX 155270560 1956217894 12.598768845813398 16.081343671028918 chrY 59373566 392086955 6.603729258909596 26.057609523747953