BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365337.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 132,362,592 number of mapped reads = 129,853,220 (98.1%) number of supplementary alignments = 1,058,467 (0.8%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 65,236,026 number of mapped paired reads (second in pair) = 64,617,194 number of mapped paired reads (both in pair) = 129,039,218 number of mapped paired reads (singletons) = 814,002 number of mapped bases = 17,190,624,424 bp number of sequenced bases = 17,184,162,776 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,219,185 duplication rate = 30.49% >>>>>>> Insert size mean insert size = 90,754.6776 std insert size = 2,972,243.5644 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 54.3449 >>>>>>> ACTG content number of A's = 5,112,363,595 bp (29.75%) number of C's = 3,419,910,447 bp (19.9%) number of T's = 5,050,644,192 bp (29.39%) number of G's = 3,600,621,794 bp (20.95%) number of N's = 622,748 bp (0%) GC percentage = 40.85% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 116,443,863 number of insertions = 5,175,402 mapped reads with insertion percentage = 3.87% number of deletions = 2,623,568 mapped reads with deletion percentage = 1.96% homopolymer indels = 50.75% >>>>>>> Coverage mean coverageData = 5.5531X std coverageData = 36.4878X There is a 73.34% of reference with a coverageData >= 1X There is a 66.35% of reference with a coverageData >= 2X There is a 57.5% of reference with a coverageData >= 3X There is a 50.78% of reference with a coverageData >= 4X There is a 43.65% of reference with a coverageData >= 5X There is a 37.93% of reference with a coverageData >= 6X There is a 32.35% of reference with a coverageData >= 7X There is a 27.81% of reference with a coverageData >= 8X There is a 23.57% of reference with a coverageData >= 9X There is a 20.1% of reference with a coverageData >= 10X There is a 16.95% of reference with a coverageData >= 11X There is a 14.36% of reference with a coverageData >= 12X There is a 12.07% of reference with a coverageData >= 13X There is a 10.18% of reference with a coverageData >= 14X There is a 8.52% of reference with a coverageData >= 15X There is a 7.17% of reference with a coverageData >= 16X There is a 5.99% of reference with a coverageData >= 17X There is a 5.03% of reference with a coverageData >= 18X There is a 4.2% of reference with a coverageData >= 19X There is a 3.52% of reference with a coverageData >= 20X There is a 2.94% of reference with a coverageData >= 21X There is a 2.47% of reference with a coverageData >= 22X There is a 2.06% of reference with a coverageData >= 23X There is a 1.73% of reference with a coverageData >= 24X There is a 1.45% of reference with a coverageData >= 25X There is a 1.22% of reference with a coverageData >= 26X There is a 1.03% of reference with a coverageData >= 27X There is a 0.87% of reference with a coverageData >= 28X There is a 0.74% of reference with a coverageData >= 29X There is a 0.63% of reference with a coverageData >= 30X There is a 0.54% of reference with a coverageData >= 31X There is a 0.46% of reference with a coverageData >= 32X There is a 0.39% of reference with a coverageData >= 33X There is a 0.34% of reference with a coverageData >= 34X There is a 0.3% of reference with a coverageData >= 35X There is a 0.26% of reference with a coverageData >= 36X There is a 0.23% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.12% of reference with a coverageData >= 43X There is a 0.11% of reference with a coverageData >= 44X There is a 0.1% of reference with a coverageData >= 45X There is a 0.09% of reference with a coverageData >= 46X There is a 0.08% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1522506141 6.108334394079604 90.32920889647339 chr2 243199373 1466973483 6.0319788858995125 25.354111792554097 chr3 198022430 1200418573 6.0620333413745096 7.065699561225587 chr4 191154276 1127992453 5.900953285502229 26.24313665100378 chr5 180915260 1063227783 5.876938092452787 7.107357328785067 chr6 171115067 1027849459 6.006773553143629 22.87669842489963 chr7 159138663 943467263 5.928586084702747 22.896845845731246 chr8 146364022 846740600 5.785168980939865 12.09299885912967 chr9 141213431 730102243 5.170203980101581 34.354669890164395 chr10 135534747 859287373 6.33997843372224 65.89542726872673 chr11 135006516 825032608 6.111057691467277 29.01532032093822 chr12 133851895 801701742 5.989468748275846 30.08711955310509 chr13 115169878 555798554 4.825902081792602 5.971881914455607 chr14 107349540 543858922 5.066243618743033 6.448500101803846 chr15 102531392 499339328 4.870111662972448 15.272149535424695 chr16 90354753 487189448 5.391962589948091 14.074616462078254 chr17 81195210 515962382 6.354591385378522 26.61089090703817 chr18 78077248 456721116 5.849605713562036 43.58438152937295 chr19 59128983 326702808 5.525256674886493 47.18257079770394 chr20 63025520 357154921 5.66683021417356 11.145863708114769 chr21 48129895 233602228 4.853578591850242 19.723978340677395 chr22 51304566 217792447 4.245088965375908 17.10590091644997 chrMT 16571 11310597 682.553678112365 153.87394983408277 chrX 155270560 433318613 2.790732596056844 10.629628888166145 chrY 59373566 136573339 2.3002381059611614 48.35779837465176