BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695947.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 153,762,738 number of mapped reads = 152,693,648 (99.3%) number of supplementary alignments = 2,059,134 (1.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 76,532,123 number of mapped paired reads (second in pair) = 76,161,525 number of mapped paired reads (both in pair) = 152,012,526 number of mapped paired reads (singletons) = 681,122 number of mapped bases = 15,147,932,008 bp number of sequenced bases = 15,143,708,102 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,655,240 duplication rate = 9.31% >>>>>>> Insert size mean insert size = 75,853.6544 std insert size = 2,705,553.1514 median insert size = 338 >>>>>>> Mapping quality mean mapping quality = 54.0614 >>>>>>> ACTG content number of A's = 4,275,020,963 bp (28.23%) number of C's = 3,258,324,302 bp (21.52%) number of T's = 4,252,035,118 bp (28.08%) number of G's = 3,358,087,639 bp (22.17%) number of N's = 240,080 bp (0%) GC percentage = 43.69% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 55,876,015 number of insertions = 2,008,379 mapped reads with insertion percentage = 1.28% number of deletions = 1,747,013 mapped reads with deletion percentage = 1.11% homopolymer indels = 44.69% >>>>>>> Coverage mean coverageData = 4.8932X std coverageData = 11.699X There is a 71.61% of reference with a coverageData >= 1X There is a 57.67% of reference with a coverageData >= 2X There is a 47.05% of reference with a coverageData >= 3X There is a 38.82% of reference with a coverageData >= 4X There is a 32.33% of reference with a coverageData >= 5X There is a 27.18% of reference with a coverageData >= 6X There is a 23.04% of reference with a coverageData >= 7X There is a 19.68% of reference with a coverageData >= 8X There is a 16.92% of reference with a coverageData >= 9X There is a 14.65% of reference with a coverageData >= 10X There is a 12.75% of reference with a coverageData >= 11X There is a 11.16% of reference with a coverageData >= 12X There is a 9.82% of reference with a coverageData >= 13X There is a 8.67% of reference with a coverageData >= 14X There is a 7.7% of reference with a coverageData >= 15X There is a 6.86% of reference with a coverageData >= 16X There is a 6.13% of reference with a coverageData >= 17X There is a 5.51% of reference with a coverageData >= 18X There is a 4.96% of reference with a coverageData >= 19X There is a 4.48% of reference with a coverageData >= 20X There is a 4.06% of reference with a coverageData >= 21X There is a 3.69% of reference with a coverageData >= 22X There is a 3.36% of reference with a coverageData >= 23X There is a 3.07% of reference with a coverageData >= 24X There is a 2.81% of reference with a coverageData >= 25X There is a 2.57% of reference with a coverageData >= 26X There is a 2.36% of reference with a coverageData >= 27X There is a 2.18% of reference with a coverageData >= 28X There is a 2.01% of reference with a coverageData >= 29X There is a 1.86% of reference with a coverageData >= 30X There is a 1.72% of reference with a coverageData >= 31X There is a 1.59% of reference with a coverageData >= 32X There is a 1.48% of reference with a coverageData >= 33X There is a 1.38% of reference with a coverageData >= 34X There is a 1.28% of reference with a coverageData >= 35X There is a 1.19% of reference with a coverageData >= 36X There is a 1.11% of reference with a coverageData >= 37X There is a 1.04% of reference with a coverageData >= 38X There is a 0.97% of reference with a coverageData >= 39X There is a 0.91% of reference with a coverageData >= 40X There is a 0.86% of reference with a coverageData >= 41X There is a 0.8% of reference with a coverageData >= 42X There is a 0.76% of reference with a coverageData >= 43X There is a 0.71% of reference with a coverageData >= 44X There is a 0.67% of reference with a coverageData >= 45X There is a 0.63% of reference with a coverageData >= 46X There is a 0.6% of reference with a coverageData >= 47X There is a 0.56% of reference with a coverageData >= 48X There is a 0.53% of reference with a coverageData >= 49X There is a 0.5% of reference with a coverageData >= 50X There is a 0.48% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1913381905 7.676538165977127 16.66673892937598 chr2 243199373 1176238606 4.836519895139697 16.560278623217265 chr3 198022430 962004141 4.858056438353978 7.3483894341809615 chr4 191154276 782351224 4.092773859790612 7.4481903295320855 chr5 180915260 851141391 4.704641228163948 7.413021363659153 chr6 171115067 560738972 3.276970180539391 7.267986329992151 chr7 159138663 1094166873 6.875556526448887 10.270515573174748 chr8 146364022 520996542 3.55959432434837 7.000446322234048 chr9 141213431 468969515 3.3209979509668597 12.815419267951858 chr10 135534747 758729829 5.5980465953870855 15.548609655957497 chr11 135006516 881722582 6.530963157363456 10.846490094892513 chr12 133851895 736132419 5.499604013824384 9.279752387891373 chr13 115169878 292922129 2.5433918493861736 6.198258377170444 chr14 107349540 494250439 4.604122560748746 9.628637156392585 chr15 102531392 337607999 3.2927281334481444 6.497116409986417 chr16 90354753 531041406 5.877293538725074 15.326810247868194 chr17 81195210 572581105 7.051907433948382 13.667309462858123 chr18 78077248 484526218 6.205728690642375 17.088569211602444 chr19 59128983 486612065 8.229670802895425 15.898000934315071 chr20 63025520 409305026 6.494274478020967 10.672272957544147 chr21 48129895 184888038 3.841438631852407 9.022008807098453 chr22 51304566 356882091 6.956146768691114 15.282893964288105 chrMT 16571 2396423 144.6154728139521 48.09254765495525 chrX 155270560 226195803 1.4567848728052504 4.674819530827654 chrY 59373566 62149267 1.0467497775019947 13.581949299182005