BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472452.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 = 25,646,294 number of mapped reads = 25,339,509 (98.8%) number of supplementary alignments = 38,930 (0.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,764,137 number of mapped paired reads (second in pair) = 12,575,372 number of mapped paired reads (both in pair) = 25,109,974 number of mapped paired reads (singletons) = 229,535 number of mapped bases = 2,495,906,280 bp number of sequenced bases = 2,495,544,768 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,223,769 duplication rate = 48.59% >>>>>>> Insert size mean insert size = 64,548.1137 std insert size = 2,510,766.2131 median insert size = 232 >>>>>>> Mapping quality mean mapping quality = 54.6331 >>>>>>> ACTG content number of A's = 702,012,429 bp (28.13%) number of C's = 545,486,968 bp (21.86%) number of T's = 707,827,149 bp (28.36%) number of G's = 539,894,470 bp (21.63%) number of N's = 323,752 bp (0.01%) GC percentage = 43.49% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 12,424,131 number of insertions = 123,672 mapped reads with insertion percentage = 0.48% number of deletions = 152,604 mapped reads with deletion percentage = 0.59% homopolymer indels = 45.7% >>>>>>> Coverage mean coverageData = 0.8063X std coverageData = 16.4945X There is a 7.43% of reference with a coverageData >= 1X There is a 2.84% of reference with a coverageData >= 2X There is a 1.17% of reference with a coverageData >= 3X There is a 0.88% of reference with a coverageData >= 4X There is a 0.7% of reference with a coverageData >= 5X There is a 0.65% of reference with a coverageData >= 6X There is a 0.61% of reference with a coverageData >= 7X There is a 0.58% of reference with a coverageData >= 8X There is a 0.56% of reference with a coverageData >= 9X There is a 0.55% of reference with a coverageData >= 10X There is a 0.54% of reference with a coverageData >= 11X There is a 0.52% of reference with a coverageData >= 12X There is a 0.51% of reference with a coverageData >= 13X There is a 0.5% of reference with a coverageData >= 14X There is a 0.49% of reference with a coverageData >= 15X There is a 0.48% of reference with a coverageData >= 16X There is a 0.47% of reference with a coverageData >= 17X There is a 0.47% of reference with a coverageData >= 18X There is a 0.46% of reference with a coverageData >= 19X There is a 0.45% of reference with a coverageData >= 20X There is a 0.44% of reference with a coverageData >= 21X There is a 0.44% of reference with a coverageData >= 22X There is a 0.43% of reference with a coverageData >= 23X There is a 0.42% of reference with a coverageData >= 24X There is a 0.42% of reference with a coverageData >= 25X There is a 0.41% of reference with a coverageData >= 26X There is a 0.41% of reference with a coverageData >= 27X There is a 0.4% of reference with a coverageData >= 28X There is a 0.4% of reference with a coverageData >= 29X There is a 0.39% of reference with a coverageData >= 30X There is a 0.39% of reference with a coverageData >= 31X There is a 0.38% of reference with a coverageData >= 32X There is a 0.38% of reference with a coverageData >= 33X There is a 0.37% of reference with a coverageData >= 34X There is a 0.37% of reference with a coverageData >= 35X There is a 0.36% of reference with a coverageData >= 36X There is a 0.36% of reference with a coverageData >= 37X There is a 0.36% of reference with a coverageData >= 38X There is a 0.35% of reference with a coverageData >= 39X There is a 0.35% of reference with a coverageData >= 40X There is a 0.34% of reference with a coverageData >= 41X There is a 0.34% of reference with a coverageData >= 42X There is a 0.34% of reference with a coverageData >= 43X There is a 0.33% of reference with a coverageData >= 44X There is a 0.33% of reference with a coverageData >= 45X There is a 0.33% of reference with a coverageData >= 46X There is a 0.32% of reference with a coverageData >= 47X There is a 0.32% of reference with a coverageData >= 48X There is a 0.32% of reference with a coverageData >= 49X There is a 0.31% of reference with a coverageData >= 50X There is a 0.31% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 214189388 0.8593334176687969 14.842041823495675 chr2 243199373 209713930 0.8623127905843737 17.817942354255255 chr3 198022430 170289756 0.8599518549489571 13.352899264776049 chr4 191154276 72731551 0.38048613152655814 9.328380276530844 chr5 180915260 93253379 0.5154533619773147 10.64847028723837 chr6 171115067 195306722 1.141376533487843 18.13627694366191 chr7 159138663 167690765 1.053739938735064 20.558700671893654 chr8 146364022 213790345 1.4606755272139214 28.067463904873172 chr9 141213431 87898572 0.6224519252704794 10.394099046167593 chr10 135534747 52093049 0.38435198466117326 8.400042620032854 chr11 135006516 76519731 0.5667854653770934 11.686614025020608 chr12 133851895 119772910 0.8948166927334126 14.259200158968845 chr13 115169878 109260438 0.9486893612928895 24.340424778114624 chr14 107349540 53030790 0.4940010921332313 10.237931909857226 chr15 102531392 48997530 0.47787832627884347 11.290051561012168 chr16 90354753 135907490 1.5041542972288353 25.66289831920782 chr17 81195210 125965020 1.551384866176219 24.13243128100158 chr18 78077248 17756092 0.22741698068046662 4.564569948602407 chr19 59128983 65222551 1.103055518475601 14.575500618203533 chr20 63025520 104668076 1.6607253061934277 33.487678537998654 chr21 48129895 24060543 0.49990848723023396 19.06388411286267 chr22 51304566 32228307 0.6281761939083551 13.010270537619004 chrMT 16571 89560 5.40462253334138 3.292511370448336 chrX 155270560 103850127 0.6688333383997584 10.607771222934277 chrY 59373566 1619658 0.02727910935987911 1.0599430517905584