BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779335.sorted.bam outfile = /home/yangyx/scDNA/SRP052954/SRP052954.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 = 148,612,570 number of mapped reads = 143,602,424 (96.63%) number of supplementary alignments = 620,196 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 72,519,248 number of mapped paired reads (second in pair) = 71,083,176 number of mapped paired reads (both in pair) = 141,373,058 number of mapped paired reads (singletons) = 2,229,366 number of mapped bases = 14,232,919,697 bp number of sequenced bases = 14,229,581,647 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,465,252 duplication rate = 6.25% >>>>>>> Insert size mean insert size = 48,407.3787 std insert size = 2,188,733.3392 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 53.9952 >>>>>>> ACTG content number of A's = 4,186,890,235 bp (29.42%) number of C's = 2,912,730,114 bp (20.47%) number of T's = 4,160,553,850 bp (29.24%) number of G's = 2,968,738,697 bp (20.86%) number of N's = 668,751 bp (0%) GC percentage = 41.33% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 56,216,756 number of insertions = 1,513,611 mapped reads with insertion percentage = 1.04% number of deletions = 1,508,963 mapped reads with deletion percentage = 1.03% homopolymer indels = 47.95% >>>>>>> Coverage mean coverageData = 4.5977X std coverageData = 7.6339X There is a 82.17% of reference with a coverageData >= 1X There is a 70.39% of reference with a coverageData >= 2X There is a 58.29% of reference with a coverageData >= 3X There is a 47.31% of reference with a coverageData >= 4X There is a 37.95% of reference with a coverageData >= 5X There is a 30.28% of reference with a coverageData >= 6X There is a 24.13% of reference with a coverageData >= 7X There is a 19.25% of reference with a coverageData >= 8X There is a 15.4% of reference with a coverageData >= 9X There is a 12.37% of reference with a coverageData >= 10X There is a 9.99% of reference with a coverageData >= 11X There is a 8.11% of reference with a coverageData >= 12X There is a 6.61% of reference with a coverageData >= 13X There is a 5.42% of reference with a coverageData >= 14X There is a 4.47% of reference with a coverageData >= 15X There is a 3.71% of reference with a coverageData >= 16X There is a 3.09% of reference with a coverageData >= 17X There is a 2.59% of reference with a coverageData >= 18X There is a 2.18% of reference with a coverageData >= 19X There is a 1.84% of reference with a coverageData >= 20X There is a 1.56% of reference with a coverageData >= 21X There is a 1.33% of reference with a coverageData >= 22X There is a 1.14% of reference with a coverageData >= 23X There is a 0.98% of reference with a coverageData >= 24X There is a 0.85% of reference with a coverageData >= 25X There is a 0.74% of reference with a coverageData >= 26X There is a 0.64% of reference with a coverageData >= 27X There is a 0.56% of reference with a coverageData >= 28X There is a 0.49% of reference with a coverageData >= 29X There is a 0.43% of reference with a coverageData >= 30X There is a 0.38% of reference with a coverageData >= 31X There is a 0.34% of reference with a coverageData >= 32X There is a 0.3% of reference with a coverageData >= 33X There is a 0.27% of reference with a coverageData >= 34X There is a 0.24% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.14% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.12% of reference with a coverageData >= 42X There is a 0.11% of reference with a coverageData >= 43X There is a 0.1% of reference with a coverageData >= 44X There is a 0.09% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.08% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.06% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1244854494 4.99438873614682 7.947592741637448 chr2 243199373 1212460280 4.985458083397279 18.29517149367806 chr3 198022430 983922226 4.968741298649855 5.054106178523414 chr4 191154276 850508873 4.449332187578164 5.614307012657553 chr5 180915260 853810735 4.719395892861663 4.85705166298246 chr6 171115067 827436726 4.8355573854872755 5.503245017162322 chr7 159138663 733616058 4.609917189011448 5.329938164119151 chr8 146364022 693959451 4.741325371613524 4.93360535649179 chr9 141213431 585698957 4.147615087689499 5.783570156009445 chr10 135534747 822747870 6.0703833386725545 8.517091389866696 chr11 135006516 681815290 5.050239871385171 5.432120549717106 chr12 133851895 656010575 4.901018211210234 5.807538849571152 chr13 115169878 406582232 3.5302827359077344 4.274138164953519 chr14 107349540 423748521 3.947371558369044 4.817384050895884 chr15 102531392 432649445 4.219677862171227 5.148812416546865 chr16 90354753 377279482 4.175535536022106 5.209029584742011 chr17 81195210 389456291 4.79654269014145 6.05133732311384 chr18 78077248 350137467 4.484500619181659 5.548972180247383 chr19 59128983 255010630 4.312785660460285 6.6334545423248 chr20 63025520 298542292 4.736847740407378 5.467875567324093 chr21 48129895 164895586 3.4260533084478992 7.845860923553333 chr22 51304566 168432330 3.2829890813227034 4.918340126997617 chrMT 16571 3776672 227.9085148753847 70.1714145203411 chrX 155270560 803697517 5.176110120295824 5.373459359992835 chrY 59373566 11869697 0.19991551459112292 2.273914493581167