BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230402.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,534,925 number of mapped reads = 3,354,032 (94.88%) number of supplementary alignments = 30,793 (0.87%) number of secondary alignments = 0 number of mapped bases = 241,057,062 bp number of sequenced bases = 240,953,732 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 209,643 duplication rate = 4.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1226 >>>>>>> ACTG content number of A's = 71,799,951 bp (29.8%) number of C's = 49,080,727 bp (20.37%) number of T's = 70,605,625 bp (29.3%) number of G's = 49,334,113 bp (20.47%) number of N's = 133,316 bp (0.06%) GC percentage = 40.84% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 2,085,685 number of insertions = 20,554 mapped reads with insertion percentage = 0.61% number of deletions = 60,979 mapped reads with deletion percentage = 1.8% homopolymer indels = 46.85% >>>>>>> Coverage mean coverageData = 0.0779X std coverageData = 0.9485X There is a 3.18% of reference with a coverageData >= 1X There is a 1.7% of reference with a coverageData >= 2X There is a 1.05% of reference with a coverageData >= 3X There is a 0.66% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 26286856 0.10546355268659491 2.1494878327941542 chr2 243199373 21833617 0.08977661714613056 0.8623678336251553 chr3 198022430 7650895 0.03863650698559754 0.38624365312459 chr4 191154276 14941881 0.07816660611871429 0.5782956513330193 chr5 180915260 9271581 0.051248197636838376 0.4477483402960355 chr6 171115067 18802724 0.10988350897235719 0.758144960179372 chr7 159138663 13734387 0.08630452676355588 1.1021330578329864 chr8 146364022 10210436 0.0697605590532351 1.0550393423152182 chr9 141213431 5646686 0.03998689048211002 0.6474813113360411 chr10 135534747 2842077 0.020969360720465284 0.5941903993261344 chr11 135006516 12840479 0.09511006861328086 0.7676248357697422 chr12 133851895 11065845 0.08267230732893248 0.5804183500030151 chr13 115169878 7640984 0.06634533380334048 0.5126544868695924 chr14 107349540 11997422 0.11176034848402704 0.6906704833042246 chr15 102531392 8722738 0.08507382792579271 0.5811955086821363 chr16 90354753 9409825 0.10414311021358223 0.7209800678026407 chr17 81195210 5044995 0.062134145597997716 0.525278459861761 chr18 78077248 3563216 0.0456370593389767 1.4824377726060733 chr19 59128983 3590802 0.0607282895428795 1.3911899553914362 chr20 63025520 8283799 0.1314356311538564 0.7529944993582225 chr21 48129895 3045913 0.06328526168611005 0.5340435340464733 chr22 51304566 3125667 0.060923758715744715 0.47531123310663775 chrMT 16571 58328 3.5198841349345242 3.173895060500287 chrX 155270560 20600063 0.13267204678079347 0.7773885933741537 chrY 59373566 845846 0.014246171435955185 0.3479575269674649