BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472431.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 13,863,672 number of mapped reads = 13,709,066 (98.88%) number of supplementary alignments = 49,568 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,883,273 number of mapped paired reads (second in pair) = 6,825,793 number of mapped paired reads (both in pair) = 13,621,140 number of mapped paired reads (singletons) = 87,926 number of mapped bases = 1,341,406,972 bp number of sequenced bases = 1,341,253,944 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,191,460 duplication rate = 47.08% >>>>>>> Insert size mean insert size = 17,734.2352 std insert size = 1,312,966.6707 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 55 >>>>>>> ACTG content number of A's = 364,210,889 bp (27.15%) number of C's = 307,476,226 bp (22.92%) number of T's = 365,450,737 bp (27.25%) number of G's = 303,950,313 bp (22.66%) number of N's = 165,779 bp (0.01%) GC percentage = 45.59% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 7,110,598 number of insertions = 74,952 mapped reads with insertion percentage = 0.54% number of deletions = 61,736 mapped reads with deletion percentage = 0.45% homopolymer indels = 46.67% >>>>>>> Coverage mean coverageData = 0.4333X std coverageData = 13.4196X There is a 3.75% of reference with a coverageData >= 1X There is a 1.69% of reference with a coverageData >= 2X There is a 0.74% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 139982199 0.5616122376682062 15.531180273011097 chr2 243199373 110707364 0.4552123742522971 13.044280776598262 chr3 198022430 93358247 0.47145289046296424 10.899969870182225 chr4 191154276 32877360 0.17199385066332495 6.047998893889022 chr5 180915260 46690608 0.25807998728244375 9.231639639256235 chr6 171115067 115004047 0.6720860355330369 15.689687226694803 chr7 159138663 100145795 0.629298959235318 20.524221490046298 chr8 146364022 111694142 0.7631256675906324 21.554523882004432 chr9 141213431 48941390 0.34657744418092923 9.51890730775849 chr10 135534747 30402172 0.22431275132715597 7.210553108659812 chr11 135006516 44352101 0.3285182250018214 10.202982031509467 chr12 133851895 70272449 0.5250015250064259 14.489112961235643 chr13 115169878 45128388 0.39184193630907554 12.050544157298289 chr14 107349540 25664587 0.23907496017216281 8.250292176494638 chr15 102531392 25536616 0.24906143866651104 7.223621875792462 chr16 90354753 71741219 0.7939949655996514 19.834246500688536 chr17 81195210 42606335 0.524739513574754 10.591661867560559 chr18 78077248 5458214 0.06990786867897802 1.9827789976272052 chr19 59128983 29513642 0.49914002410628305 10.312188028561305 chr20 63025520 70223461 1.1142067689405815 31.30192925695621 chr21 48129895 8353061 0.17355244593822614 7.92262642234976 chr22 51304566 10318074 0.2011141464484857 5.525634532127927 chrMT 16571 626 0.03777683905618249 0.2119408800143469 chrX 155270560 62231695 0.40079519903837535 12.375448487072509 chrY 59373566 203180 0.003422061595559209 0.23099774547755267