BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1778461.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 = 203,204,212 number of mapped reads = 193,298,758 (95.13%) number of supplementary alignments = 432,877 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 97,251,256 number of mapped paired reads (second in pair) = 96,047,502 number of mapped paired reads (both in pair) = 191,158,150 number of mapped paired reads (singletons) = 2,140,608 number of mapped bases = 14,320,718,282 bp number of sequenced bases = 14,319,429,413 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 151,098,519 duplication rate = 62.52% >>>>>>> Insert size mean insert size = 30,493.5957 std insert size = 1,733,455.2049 median insert size = 89 >>>>>>> Mapping quality mean mapping quality = 51.9254 >>>>>>> ACTG content number of A's = 3,485,548,122 bp (24.34%) number of C's = 3,694,722,306 bp (25.8%) number of T's = 3,434,577,984 bp (23.99%) number of G's = 3,702,541,361 bp (25.86%) number of N's = 2,039,640 bp (0.01%) GC percentage = 51.66% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 70,189,409 number of insertions = 430,787 mapped reads with insertion percentage = 0.22% number of deletions = 593,148 mapped reads with deletion percentage = 0.3% homopolymer indels = 33.03% >>>>>>> Coverage mean coverageData = 4.626X std coverageData = 60.1845X There is a 11.49% of reference with a coverageData >= 1X There is a 8.38% of reference with a coverageData >= 2X There is a 5.91% of reference with a coverageData >= 3X There is a 5.36% of reference with a coverageData >= 4X There is a 4.41% of reference with a coverageData >= 5X There is a 4.14% of reference with a coverageData >= 6X There is a 3.63% of reference with a coverageData >= 7X There is a 3.46% of reference with a coverageData >= 8X There is a 3.14% of reference with a coverageData >= 9X There is a 3.02% of reference with a coverageData >= 10X There is a 2.81% of reference with a coverageData >= 11X There is a 2.72% of reference with a coverageData >= 12X There is a 2.58% of reference with a coverageData >= 13X There is a 2.51% of reference with a coverageData >= 14X There is a 2.4% of reference with a coverageData >= 15X There is a 2.34% of reference with a coverageData >= 16X There is a 2.26% of reference with a coverageData >= 17X There is a 2.21% of reference with a coverageData >= 18X There is a 2.15% of reference with a coverageData >= 19X There is a 2.11% of reference with a coverageData >= 20X There is a 2.06% of reference with a coverageData >= 21X There is a 2.03% of reference with a coverageData >= 22X There is a 1.99% of reference with a coverageData >= 23X There is a 1.96% of reference with a coverageData >= 24X There is a 1.92% of reference with a coverageData >= 25X There is a 1.9% of reference with a coverageData >= 26X There is a 1.87% of reference with a coverageData >= 27X There is a 1.84% of reference with a coverageData >= 28X There is a 1.82% of reference with a coverageData >= 29X There is a 1.8% of reference with a coverageData >= 30X There is a 1.78% of reference with a coverageData >= 31X There is a 1.76% of reference with a coverageData >= 32X There is a 1.74% of reference with a coverageData >= 33X There is a 1.72% of reference with a coverageData >= 34X There is a 1.7% of reference with a coverageData >= 35X There is a 1.68% of reference with a coverageData >= 36X There is a 1.67% of reference with a coverageData >= 37X There is a 1.65% of reference with a coverageData >= 38X There is a 1.64% of reference with a coverageData >= 39X There is a 1.62% of reference with a coverageData >= 40X There is a 1.61% of reference with a coverageData >= 41X There is a 1.59% of reference with a coverageData >= 42X There is a 1.58% of reference with a coverageData >= 43X There is a 1.57% of reference with a coverageData >= 44X There is a 1.55% of reference with a coverageData >= 45X There is a 1.54% of reference with a coverageData >= 46X There is a 1.53% of reference with a coverageData >= 47X There is a 1.52% of reference with a coverageData >= 48X There is a 1.51% of reference with a coverageData >= 49X There is a 1.49% of reference with a coverageData >= 50X There is a 1.48% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1700156636 6.821072818911853 92.81874775377138 chr2 243199373 999872988 4.111330451497505 50.62401594734861 chr3 198022430 770475686 3.890850576876569 51.17199425484531 chr4 191154276 552437914 2.8900107575935157 42.22361369465291 chr5 180915260 624936970 3.4543076686842227 41.84457390252503 chr6 171115067 727864111 4.253652958567348 68.30949232184676 chr7 159138663 726106794 4.562730264989093 67.70867557358412 chr8 146364022 446682348 3.051858932928203 38.15057328535791 chr9 141213431 605594899 4.288507790735571 48.53054029470986 chr10 135534747 586944191 4.330580932135432 47.03385335050249 chr11 135006516 804887743 5.9618436713084275 61.379797724469014 chr12 133851895 704307800 5.261844070268859 52.606314781969495 chr13 115169878 232574936 2.0194076788029593 33.06985307411537 chr14 107349540 459716739 4.282428587956688 51.75563991265616 chr15 102531392 533613398 5.20439045633946 55.664277941936355 chr16 90354753 636741437 7.047127194293807 63.89130814268282 chr17 81195210 898454843 11.06536756293875 133.16221901833234 chr18 78077248 206128674 2.640060699885324 36.671859264936316 chr19 59128983 861072287 14.562609456685564 95.24840270490813 chr20 63025520 329883500 5.234125795392089 49.87210565383969 chr21 48129895 159981965 3.3239624769594864 45.858972136480176 chr22 51304566 317379266 6.186179725211982 58.57376706551306 chrMT 16571 180672 10.902902661275723 12.004094050722127 chrX 155270560 370166287 2.3840081918942007 41.387911542675525 chrY 59373566 64556198 1.08728854184032 44.41494074153152