BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548938.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,452,628 number of mapped reads = 7,357,570 (87.04%) number of secondary alignments = 0 number of mapped bases = 291,222,480 bp number of sequenced bases = 291,190,460 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 254,615 duplication rate = 2.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9407 >>>>>>> ACTG content number of A's = 85,922,308 bp (29.51%) number of C's = 59,596,173 bp (20.47%) number of T's = 86,194,092 bp (29.6%) number of G's = 59,475,190 bp (20.42%) number of N's = 2,697 bp (0%) GC percentage = 40.89% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 809,799 number of insertions = 9,631 mapped reads with insertion percentage = 0.13% number of deletions = 24,110 mapped reads with deletion percentage = 0.33% homopolymer indels = 41.01% >>>>>>> Coverage mean coverageData = 0.0941X std coverageData = 1.1069X There is a 7.7% of reference with a coverageData >= 1X There is a 1.26% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 22793893 0.09144969392072247 1.0223688553618273 chr2 243199373 24794993 0.10195335906560911 0.5401865984338566 chr3 198022430 19925050 0.10062016711945207 0.3724429038804688 chr4 191154276 19518918 0.10211081022325653 0.3866511274899192 chr5 180915260 18289762 0.10109573951915389 0.3807524807770086 chr6 171115067 17262623 0.10088312679093303 0.4193219513299652 chr7 159138663 16109952 0.10123216882876539 0.7785633956645094 chr8 146364022 15460401 0.10562979063256406 4.437145140108018 chr9 141213431 12159851 0.08610973413711617 0.5073472558957292 chr10 135534747 13415570 0.0989825140559712 0.49347071795955855 chr11 135006516 13243116 0.09809242096137048 0.5816754382611194 chr12 133851895 13188297 0.09852902717589467 0.38300601436919074 chr13 115169878 9642188 0.08372143973270511 0.33463998390981414 chr14 107349540 8944547 0.08332170775953023 0.4091568124617532 chr15 102531392 8217421 0.08014541536703218 0.33085059723589455 chr16 90354753 7754477 0.08582256873636741 0.37723694944585306 chr17 81195210 7298884 0.08989303679367293 0.3784608468635583 chr18 78077248 7761875 0.09941276362609502 0.9046592624259904 chr19 59128983 5293558 0.0895256054040368 0.8957428832116994 chr20 63025520 5720597 0.09076635940488868 0.36673975121943625 chr21 48129895 3695202 0.0767756090055879 0.3653453602889974 chr22 51304566 3084177 0.060115058764945016 0.3361310994147257 chrMT 16571 13876 0.8373664836159556 1.2154023021843972 chrX 155270560 16777590 0.10805390281325707 0.47186322640862405 chrY 59373566 855662 0.014411497534104655 0.19297988574412303