BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472539.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,530,364 number of mapped reads = 18,333,035 (98.94%) number of supplementary alignments = 78,088 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,197,332 number of mapped paired reads (second in pair) = 9,135,703 number of mapped paired reads (both in pair) = 18,222,274 number of mapped paired reads (singletons) = 110,761 number of mapped bases = 1,800,120,388 bp number of sequenced bases = 1,799,898,799 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,676,376 duplication rate = 46.68% >>>>>>> Insert size mean insert size = 31,789.1585 std insert size = 1,763,145.7143 median insert size = 215 >>>>>>> Mapping quality mean mapping quality = 55.1865 >>>>>>> ACTG content number of A's = 486,707,225 bp (27.04%) number of C's = 415,969,932 bp (23.11%) number of T's = 483,908,498 bp (26.89%) number of G's = 413,029,113 bp (22.95%) number of N's = 284,031 bp (0.02%) GC percentage = 46.06% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 9,993,355 number of insertions = 87,481 mapped reads with insertion percentage = 0.47% number of deletions = 83,430 mapped reads with deletion percentage = 0.45% homopolymer indels = 44.84% >>>>>>> Coverage mean coverageData = 0.5815X std coverageData = 18.7127X There is a 5.62% of reference with a coverageData >= 1X There is a 2.59% of reference with a coverageData >= 2X There is a 1.08% of reference with a coverageData >= 3X There is a 0.76% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 171514600 0.6881210538689089 22.565869952703448 chr2 243199373 122118846 0.5021347073949899 17.615531003879948 chr3 198022430 196675936 0.9932002955422777 22.243338724030643 chr4 191154276 72804820 0.3808694292561889 14.638235167531631 chr5 180915260 103857016 0.5740644321545899 21.347040136957354 chr6 171115067 120579540 0.7046693322453014 19.55842643715296 chr7 159138663 64903846 0.40784461033205993 13.850649066686866 chr8 146364022 99481254 0.6796837955163599 21.666282070028647 chr9 141213431 106233273 0.7522887323656912 20.88424922635964 chr10 135534747 49429414 0.36469920145274626 14.194512254287579 chr11 135006516 89414946 0.6623009662733612 19.369054515218327 chr12 133851895 96681432 0.7223015557605665 17.732787994371225 chr13 115169878 32225307 0.2798067303674664 9.743094501060364 chr14 107349540 46582621 0.43393405318737277 16.28610831451212 chr15 102531392 52314803 0.510232056539328 21.64747608448927 chr16 90354753 75016954 0.8302491181620517 28.289989768869113 chr17 81195210 65375905 0.8051694798252261 19.174625717557095 chr18 78077248 24625644 0.3154010243803675 11.374675332567508 chr19 59128983 48513738 0.8204730664824728 24.522310526630445 chr20 63025520 36483156 0.5788632287365499 16.184083631978858 chr21 48129895 11575991 0.240515608853915 11.484164563334371 chr22 51304566 20708610 0.40364068180598195 14.167169280335102 chrMT 16571 1636 0.09872669120753123 0.44561056175390906 chrX 155270560 90045504 0.5799264458117495 17.046604242062937 chrY 59373566 2955596 0.04977966120478598 1.9743775647447779