BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472734.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 = 14,513,370 number of mapped reads = 14,313,242 (98.62%) number of supplementary alignments = 49,149 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,201,493 number of mapped paired reads (second in pair) = 7,111,749 number of mapped paired reads (both in pair) = 14,190,530 number of mapped paired reads (singletons) = 122,712 number of mapped bases = 1,410,193,664 bp number of sequenced bases = 1,409,992,553 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,412,716 duplication rate = 45.84% >>>>>>> Insert size mean insert size = 22,824.169 std insert size = 1,494,418.8668 median insert size = 254 >>>>>>> Mapping quality mean mapping quality = 55.3472 >>>>>>> ACTG content number of A's = 394,736,750 bp (28%) number of C's = 313,649,278 bp (22.24%) number of T's = 390,613,147 bp (27.7%) number of G's = 310,735,492 bp (22.04%) number of N's = 257,886 bp (0.02%) GC percentage = 44.28% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 11,142,002 number of insertions = 84,401 mapped reads with insertion percentage = 0.58% number of deletions = 82,934 mapped reads with deletion percentage = 0.57% homopolymer indels = 45.39% >>>>>>> Coverage mean coverageData = 0.4555X std coverageData = 13.9229X There is a 4.23% of reference with a coverageData >= 1X There is a 1.76% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% 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 0.18% of reference with a coverageData >= 43X There is a 0.18% 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 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% 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 141242478 0.5666685099251969 16.496029494621133 chr2 243199373 99100692 0.40748744857989416 14.712843761813314 chr3 198022430 173893009 0.8781480411082724 18.73279957719358 chr4 191154276 59720854 0.3124222761305115 13.386087227681191 chr5 180915260 79268481 0.438152541692724 14.250025617078437 chr6 171115067 96268747 0.5625965538148666 17.250234353471512 chr7 159138663 49887822 0.31348649699287723 9.208239293629132 chr8 146364022 59217957 0.40459367125071216 13.28761287589773 chr9 141213431 76170665 0.5394009936632728 11.979646643194227 chr10 135534747 47089822 0.3474372664007703 12.644959821001578 chr11 135006516 58801621 0.4355465405832708 12.18387484245872 chr12 133851895 70472595 0.5264968045465475 14.592190513991069 chr13 115169878 33565867 0.29144657946064684 10.747776618219653 chr14 107349540 36819051 0.3429828483661877 11.093513041889224 chr15 102531392 35041288 0.34176155532931807 11.775367074972605 chr16 90354753 45352580 0.5019390623534769 12.380179571286659 chr17 81195210 54600346 0.6724577225676244 14.028962340944977 chr18 78077248 32537517 0.416734936661702 18.822439470797374 chr19 59128983 39725469 0.6718442798179025 17.36401627670391 chr20 63025520 25764321 0.4087918830340472 10.672618051569282 chr21 48129895 6400996 0.13299418168271507 6.034507064703115 chr22 51304566 11349751 0.22122301940922764 6.147141084264703 chrMT 16571 3337 0.2013758976525255 0.5533410862031973 chrX 155270560 75335665 0.48518962641726804 14.173158449583791 chrY 59373566 2562733 0.04316286139862308 1.8976596180162526