BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472626.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 = 18,724,004 number of mapped reads = 18,573,711 (99.2%) number of supplementary alignments = 82,505 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,317,444 number of mapped paired reads (second in pair) = 9,256,267 number of mapped paired reads (both in pair) = 18,470,340 number of mapped paired reads (singletons) = 103,371 number of mapped bases = 1,822,446,514 bp number of sequenced bases = 1,822,215,307 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,085,020 duplication rate = 50.6% >>>>>>> Insert size mean insert size = 19,339.6379 std insert size = 1,404,037.1716 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 54.7477 >>>>>>> ACTG content number of A's = 488,678,512 bp (26.82%) number of C's = 424,069,917 bp (23.27%) number of T's = 489,784,456 bp (26.88%) number of G's = 419,335,935 bp (23.01%) number of N's = 346,487 bp (0.02%) GC percentage = 46.28% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 10,369,858 number of insertions = 95,731 mapped reads with insertion percentage = 0.51% number of deletions = 92,922 mapped reads with deletion percentage = 0.49% homopolymer indels = 47.19% >>>>>>> Coverage mean coverageData = 0.5887X std coverageData = 25.8406X There is a 3.58% of reference with a coverageData >= 1X There is a 1.67% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% 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 0.16% of reference with a coverageData >= 45X There is a 0.16% 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 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 257575015 1.033397686098443 36.77345305055359 chr2 243199373 126244219 0.5190976335288496 20.845299754163563 chr3 198022430 123350510 0.6229118085259332 21.25418412106367 chr4 191154276 68771035 0.3597671809340012 32.66862571220927 chr5 180915260 85239239 0.47115560622138786 19.597936208344255 chr6 171115067 151179996 0.883499031677906 31.00991667287367 chr7 159138663 97785701 0.6144685342744145 31.862025358065647 chr8 146364022 137059100 0.9364261662609955 37.93324980599969 chr9 141213431 87035716 0.616341628297382 22.70685144214262 chr10 135534747 47532310 0.35070202329739103 15.375754967372497 chr11 135006516 42970707 0.31828617072082654 14.530781235750986 chr12 133851895 48735206 0.3640979905439516 12.595029538095705 chr13 115169878 84858451 0.736811156472702 42.226906883269145 chr14 107349540 24833025 0.23132865776602304 9.44757625353764 chr15 102531392 21967480 0.21425126072608086 14.488664236552284 chr16 90354753 76421799 0.8457972210936153 30.998260002580672 chr17 81195210 59855595 0.7371813558952554 17.385909518301236 chr18 78077248 12528625 0.1604644799980655 7.6902013689915005 chr19 59128983 49748511 0.8413557696400765 27.07195268396323 chr20 63025520 73979236 1.173798105910114 30.947627412303028 chr21 48129895 14658117 0.30455327193213283 20.2960491036448 chr22 51304566 25211450 0.49140752891272876 18.630156571687543 chrMT 16571 4950 0.2987146219298775 0.8561830769140911 chrX 155270560 104551828 0.6733525531176032 22.138507409401093 chrY 59373566 348693 0.005872866049514358 0.5363996798241769