BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617646.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,703,397 (95.95%) number of supplementary alignments = 141,864 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,360,811 number of mapped paired reads (second in pair) = 15,342,586 number of mapped paired reads (both in pair) = 30,270,672 number of mapped paired reads (singletons) = 432,725 number of mapped bases = 2,993,143,083 bp number of sequenced bases = 2,991,311,766 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,204,308 duplication rate = 10.95% >>>>>>> Insert size mean insert size = 30,907.7863 std insert size = 1,606,343.6827 median insert size = 227 >>>>>>> Mapping quality mean mapping quality = 52.7535 >>>>>>> ACTG content number of A's = 888,790,605 bp (29.71%) number of C's = 597,757,610 bp (19.98%) number of T's = 888,458,227 bp (29.7%) number of G's = 614,156,730 bp (20.53%) number of N's = 2,148,594 bp (0.07%) GC percentage = 40.51% >>>>>>> Mismatches and indels general error rate = 0.0139 number of mismatches = 40,524,515 number of insertions = 467,401 mapped reads with insertion percentage = 1.49% number of deletions = 1,101,813 mapped reads with deletion percentage = 3.51% homopolymer indels = 47.72% >>>>>>> Coverage mean coverageData = 0.9669X std coverageData = 10.8793X There is a 33.59% of reference with a coverageData >= 1X There is a 19.57% of reference with a coverageData >= 2X There is a 12.03% of reference with a coverageData >= 3X There is a 7.73% of reference with a coverageData >= 4X There is a 5.11% of reference with a coverageData >= 5X There is a 3.48% of reference with a coverageData >= 6X There is a 2.42% of reference with a coverageData >= 7X There is a 1.72% of reference with a coverageData >= 8X There is a 1.25% of reference with a coverageData >= 9X There is a 0.93% of reference with a coverageData >= 10X There is a 0.7% of reference with a coverageData >= 11X There is a 0.53% of reference with a coverageData >= 12X There is a 0.42% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.18% of reference with a coverageData >= 17X There is a 0.15% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 183572662 0.7364983134786252 10.506328118449865 chr2 243199373 309029098 1.2706821328852687 12.446082287472294 chr3 198022430 250582978 1.265427244782321 2.5088443657755644 chr4 191154276 167208172 0.8747289126820266 8.734558316136383 chr5 180915260 198023581 1.094565383815605 2.3684546710165577 chr6 171115067 144740917 0.8458689204732626 5.802007425539143 chr7 159138663 233895256 1.469757578646994 13.629278278002051 chr8 146364022 132860338 0.9077390480564957 4.136746774185252 chr9 141213431 123151307 0.8720934413101258 21.407828092726938 chr10 135534747 126923891 0.9364675392060163 21.81459880898938 chr11 135006516 164924428 1.2216034669022937 12.26319802255867 chr12 133851895 127915944 0.9556528430172767 2.1728131484196975 chr13 115169878 128405320 1.1149210386417185 2.324565595530473 chr14 107349540 85607193 0.7974621316495627 2.49938755284476 chr15 102531392 64035463 0.6245449491215335 1.6002172769937055 chr16 90354753 82686348 0.9151300319530506 16.87496274678346 chr17 81195210 74241726 0.9143609087284829 13.230435716044298 chr18 78077248 55137699 0.7061941911682134 18.762299210174053 chr19 59128983 31826877 0.538261870663326 6.199663234553422 chr20 63025520 81317952 1.2902384938672462 3.0979702967258707 chr21 48129895 43801415 0.9100667059423254 4.532262050807108 chr22 51304566 19372855 0.377604889981917 1.2899008070249927 chrMT 16571 3174287 191.5567557781667 133.83371733678592 chrX 155270560 148577034 0.956891209769579 4.428817973439365 chrY 59373566 12130342 0.20430543114085484 18.035440350345194