BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504410.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 132,806,906 number of mapped reads = 131,909,933 (99.32%) number of supplementary alignments = 2,230,315 (1.68%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 66,018,472 number of mapped paired reads (second in pair) = 65,891,461 number of mapped paired reads (both in pair) = 131,612,634 number of mapped paired reads (singletons) = 297,299 number of mapped bases = 12,593,097,375 bp number of sequenced bases = 12,589,014,271 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,319,451 duplication rate = 27.81% >>>>>>> Insert size mean insert size = 83,893.3438 std insert size = 2,773,569.3647 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 52.6524 >>>>>>> ACTG content number of A's = 3,746,484,311 bp (29.76%) number of C's = 2,533,811,332 bp (20.13%) number of T's = 3,765,927,530 bp (29.91%) number of G's = 2,540,868,449 bp (20.18%) number of N's = 1,922,649 bp (0.02%) GC percentage = 40.31% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 63,268,057 number of insertions = 1,315,256 mapped reads with insertion percentage = 0.99% number of deletions = 2,606,182 mapped reads with deletion percentage = 1.95% homopolymer indels = 49.13% >>>>>>> Coverage mean coverageData = 4.0679X std coverageData = 250.7171X There is a 26.99% of reference with a coverageData >= 1X There is a 20.58% of reference with a coverageData >= 2X There is a 15.9% of reference with a coverageData >= 3X There is a 13.34% of reference with a coverageData >= 4X There is a 11.37% of reference with a coverageData >= 5X There is a 9.97% of reference with a coverageData >= 6X There is a 8.85% of reference with a coverageData >= 7X There is a 7.96% of reference with a coverageData >= 8X There is a 7.22% of reference with a coverageData >= 9X There is a 6.6% of reference with a coverageData >= 10X There is a 6.07% of reference with a coverageData >= 11X There is a 5.62% of reference with a coverageData >= 12X There is a 5.23% of reference with a coverageData >= 13X There is a 4.88% of reference with a coverageData >= 14X There is a 4.57% of reference with a coverageData >= 15X There is a 4.3% of reference with a coverageData >= 16X There is a 4.05% of reference with a coverageData >= 17X There is a 3.83% of reference with a coverageData >= 18X There is a 3.63% of reference with a coverageData >= 19X There is a 3.44% of reference with a coverageData >= 20X There is a 3.28% of reference with a coverageData >= 21X There is a 3.12% of reference with a coverageData >= 22X There is a 2.98% of reference with a coverageData >= 23X There is a 2.85% of reference with a coverageData >= 24X There is a 2.73% of reference with a coverageData >= 25X There is a 2.62% of reference with a coverageData >= 26X There is a 2.51% of reference with a coverageData >= 27X There is a 2.41% of reference with a coverageData >= 28X There is a 2.32% of reference with a coverageData >= 29X There is a 2.24% of reference with a coverageData >= 30X There is a 2.16% of reference with a coverageData >= 31X There is a 2.08% of reference with a coverageData >= 32X There is a 2.01% of reference with a coverageData >= 33X There is a 1.94% of reference with a coverageData >= 34X There is a 1.88% of reference with a coverageData >= 35X There is a 1.82% of reference with a coverageData >= 36X There is a 1.76% of reference with a coverageData >= 37X There is a 1.71% of reference with a coverageData >= 38X There is a 1.66% of reference with a coverageData >= 39X There is a 1.61% of reference with a coverageData >= 40X There is a 1.56% of reference with a coverageData >= 41X There is a 1.52% of reference with a coverageData >= 42X There is a 1.48% of reference with a coverageData >= 43X There is a 1.44% of reference with a coverageData >= 44X There is a 1.4% of reference with a coverageData >= 45X There is a 1.36% of reference with a coverageData >= 46X There is a 1.33% of reference with a coverageData >= 47X There is a 1.3% of reference with a coverageData >= 48X There is a 1.26% of reference with a coverageData >= 49X There is a 1.23% of reference with a coverageData >= 50X There is a 1.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 845915912 3.3938367278932478 27.04453058071725 chr2 243199373 926550845 3.809840599383453 28.828570144395933 chr3 198022430 698309507 3.5264162095172753 21.195892644367422 chr4 191154276 783443840 4.0984897455288944 29.553582192093028 chr5 180915260 784499743 4.336282870776075 36.66116605806935 chr6 171115067 2348968709 13.727421846493506 1051.6802569818944 chr7 159138663 546208463 3.4322800801713407 25.84960102801395 chr8 146364022 574912984 3.9279665599787905 26.93522276110155 chr9 141213431 422380611 2.9910795878899084 20.34745396724328 chr10 135534747 442913098 3.2678933469363396 19.338357240835315 chr11 135006516 549726079 4.0718484950756 45.38338162745645 chr12 133851895 477153206 3.564784839243404 25.228208567969602 chr13 115169878 565541718 4.910500278553738 167.4921900393045 chr14 107349540 297285762 2.7693249733534024 16.203491164717473 chr15 102531392 261086978 2.5464101569985513 16.490795155422056 chr16 90354753 221121086 2.4472546120512333 30.56517978542364 chr17 81195210 203905472 2.511299274920282 18.129317702807473 chr18 78077248 287178788 3.6781366576854757 31.004285784689976 chr19 59128983 111905586 1.8925674064104907 19.379790763265017 chr20 63025520 176306854 2.797388327775796 17.809802580958777 chr21 48129895 104268737 2.166402752384978 13.302548749072542 chr22 51304566 60046713 1.170397055887774 9.596163471026868 chrMT 16571 13044 0.7871582885764287 4.065498164721495 chrX 155270560 893539283 5.75472441781623 37.332997074218575 chrY 59373566 9914357 0.16698267710583528 3.0217473955372696