BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053606.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 4,969,157 number of mapped reads = 2,927,375 (58.91%) number of supplementary alignments = 69 (0%) number of secondary alignments = 0 number of mapped bases = 137,594,234 bp number of sequenced bases = 137,568,107 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 375,244 duplication rate = 10.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8659 >>>>>>> ACTG content number of A's = 40,941,187 bp (29.76%) number of C's = 26,558,572 bp (19.31%) number of T's = 40,865,393 bp (29.71%) number of G's = 28,850,733 bp (20.97%) number of N's = 352,222 bp (0.26%) GC percentage = 40.28% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 1,425,990 number of insertions = 6,635 mapped reads with insertion percentage = 0.23% number of deletions = 18,138 mapped reads with deletion percentage = 0.62% homopolymer indels = 45.44% >>>>>>> Coverage mean coverageData = 0.0444X std coverageData = 0.4278X There is a 2.8% of reference with a coverageData >= 1X There is a 0.83% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 10896397 0.04371662929578017 0.37631928293037875 chr2 243199373 11759622 0.048353833543806055 0.9034787138470374 chr3 198022430 9601219 0.048485512474521195 0.36133760931362446 chr4 191154276 9089089 0.04754844720292838 0.3712656797047526 chr5 180915260 8589588 0.047478515632125226 0.3542561944875902 chr6 171115067 8232812 0.048112724053691894 0.3846318932796017 chr7 159138663 7408041 0.04655085609208618 0.395595238583257 chr8 146364022 7046868 0.0481461762508822 0.36841374580529346 chr9 141213431 5679700 0.0402206784424068 0.337530069350246 chr10 135534747 6289615 0.046405922755734366 0.36660041625841117 chr11 135006516 6224375 0.046104256182716394 0.37040404852762165 chr12 133851895 6268062 0.04682833963613291 0.3511566777267553 chr13 115169878 4534596 0.039373107610654934 0.32290991734913 chr14 107349540 4186311 0.03899700920935479 0.3426107831761786 chr15 102531392 3972405 0.03874330507480089 0.31761065545781425 chr16 90354753 3757878 0.04159026365774029 0.3444726167453085 chr17 81195210 3393634 0.04179598771897997 0.32457751575175564 chr18 78077248 3648532 0.0467297720329487 0.3825936442190133 chr19 59128983 2235143 0.03780114060138663 0.3475617784279041 chr20 63025520 2892384 0.045892267132425085 0.3556545712015315 chr21 48129895 1768203 0.03673814372543302 0.337730439520941 chr22 51304566 1433126 0.027933693075193347 0.26589195500148166 chrMT 16571 26761 1.614929696457667 2.781896355517196 chrX 155270560 8316198 0.053559399798648245 0.41816845097891836 chrY 59373566 343675 0.005788350324115617 0.12680320840183112