BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777290.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 102,540,314 number of mapped reads = 100,841,214 (98.34%) number of supplementary alignments = 4,863,257 (4.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 50,565,502 number of mapped paired reads (second in pair) = 50,275,712 number of mapped paired reads (both in pair) = 100,323,292 number of mapped paired reads (singletons) = 517,922 number of mapped bases = 9,747,862,865 bp number of sequenced bases = 9,744,812,320 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,635,175 duplication rate = 12.72% >>>>>>> Insert size mean insert size = 145,482.6821 std insert size = 3,659,520.784 median insert size = 155 >>>>>>> Mapping quality mean mapping quality = 52.9956 >>>>>>> ACTG content number of A's = 2,847,201,520 bp (29.22%) number of C's = 2,027,997,375 bp (20.81%) number of T's = 2,780,554,577 bp (28.53%) number of G's = 2,088,897,120 bp (21.44%) number of N's = 161,728 bp (0%) GC percentage = 42.25% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 59,643,598 number of insertions = 2,224,755 mapped reads with insertion percentage = 2.16% number of deletions = 1,222,445 mapped reads with deletion percentage = 1.18% homopolymer indels = 46.38% >>>>>>> Coverage mean coverageData = 3.1488X std coverageData = 28.4806X There is a 52.54% of reference with a coverageData >= 1X There is a 41.51% of reference with a coverageData >= 2X There is a 32.56% of reference with a coverageData >= 3X There is a 26.4% of reference with a coverageData >= 4X There is a 21.63% of reference with a coverageData >= 5X There is a 17.94% of reference with a coverageData >= 6X There is a 15% of reference with a coverageData >= 7X There is a 12.64% of reference with a coverageData >= 8X There is a 10.72% of reference with a coverageData >= 9X There is a 9.13% of reference with a coverageData >= 10X There is a 7.81% of reference with a coverageData >= 11X There is a 6.71% of reference with a coverageData >= 12X There is a 5.78% of reference with a coverageData >= 13X There is a 5% of reference with a coverageData >= 14X There is a 4.33% of reference with a coverageData >= 15X There is a 3.76% of reference with a coverageData >= 16X There is a 3.27% of reference with a coverageData >= 17X There is a 2.85% of reference with a coverageData >= 18X There is a 2.49% of reference with a coverageData >= 19X There is a 2.18% of reference with a coverageData >= 20X There is a 1.91% of reference with a coverageData >= 21X There is a 1.68% of reference with a coverageData >= 22X There is a 1.48% of reference with a coverageData >= 23X There is a 1.31% of reference with a coverageData >= 24X There is a 1.15% of reference with a coverageData >= 25X There is a 1.02% of reference with a coverageData >= 26X There is a 0.91% of reference with a coverageData >= 27X There is a 0.8% of reference with a coverageData >= 28X There is a 0.72% of reference with a coverageData >= 29X There is a 0.64% of reference with a coverageData >= 30X There is a 0.57% of reference with a coverageData >= 31X There is a 0.51% of reference with a coverageData >= 32X There is a 0.46% of reference with a coverageData >= 33X There is a 0.41% of reference with a coverageData >= 34X There is a 0.37% of reference with a coverageData >= 35X There is a 0.33% of reference with a coverageData >= 36X There is a 0.3% of reference with a coverageData >= 37X There is a 0.27% of reference with a coverageData >= 38X There is a 0.25% of reference with a coverageData >= 39X There is a 0.22% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 803895200 3.225248534084896 61.255150989963795 chr2 243199373 836145934 3.4381089214403526 19.479365828281672 chr3 198022430 653359761 3.2994230047575925 6.807152873371953 chr4 191154276 639109622 3.3434230997793635 22.835496751379793 chr5 180915260 590925896 3.2663131678333825 5.9472779974338135 chr6 171115067 566400390 3.3100556247335016 13.271561584160642 chr7 159138663 526735472 3.309915152422765 26.110789542250636 chr8 146364022 497314341 3.3977908929012623 14.255551827450013 chr9 141213431 409004041 2.8963536832413626 24.826079536750413 chr10 135534747 496241139 3.6613573270624102 44.94173896877301 chr11 135006516 461503223 3.4183773989101387 22.077307596205774 chr12 133851895 437182452 3.266165578006946 5.848614033057395 chr13 115169878 304362950 2.642730506322148 5.266184147961641 chr14 107349540 297333656 2.769771123378824 5.804976032363407 chr15 102531392 277778126 2.709200768482691 5.248656382643942 chr16 90354753 295629796 3.2718787466554193 12.30947321527495 chr17 81195210 274412378 3.3796621500209185 14.375135598480767 chr18 78077248 269362032 3.4499427028985448 38.194726104439084 chr19 59128983 187922814 3.1781844446741117 32.789612903069695 chr20 63025520 215533241 3.4197772743485495 8.496268971155441 chr21 48129895 134491353 2.794341292454513 12.909903119947273 chr22 51304566 119613759 2.331444710008852 6.604069792687238 chrMT 16571 87503731 5280.534125882566 1174.4679496894228 chrX 155270560 273085376 1.758771115400112 9.461253959769367 chrY 59373566 93016182 1.5666261649165556 25.143453570293413