BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472406.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 = 18,674,906 number of mapped reads = 18,516,451 (99.15%) number of supplementary alignments = 98,539 (0.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,286,193 number of mapped paired reads (second in pair) = 9,230,258 number of mapped paired reads (both in pair) = 18,420,474 number of mapped paired reads (singletons) = 95,977 number of mapped bases = 1,816,183,227 bp number of sequenced bases = 1,815,961,257 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,526,324 duplication rate = 45.12% >>>>>>> Insert size mean insert size = 15,797.3216 std insert size = 1,135,373.0775 median insert size = 214 >>>>>>> Mapping quality mean mapping quality = 54.145 >>>>>>> ACTG content number of A's = 491,816,167 bp (27.08%) number of C's = 417,494,979 bp (22.99%) number of T's = 492,738,300 bp (27.13%) number of G's = 413,690,653 bp (22.78%) number of N's = 221,158 bp (0.01%) GC percentage = 45.77% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 9,646,345 number of insertions = 106,876 mapped reads with insertion percentage = 0.57% number of deletions = 90,173 mapped reads with deletion percentage = 0.48% homopolymer indels = 49.06% >>>>>>> Coverage mean coverageData = 0.5867X std coverageData = 36.1867X There is a 4.29% of reference with a coverageData >= 1X There is a 2.05% of reference with a coverageData >= 2X There is a 0.95% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.29% of reference with a coverageData >= 8X There is a 0.27% of reference with a coverageData >= 9X There is a 0.25% of reference with a coverageData >= 10X There is a 0.24% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.19% of reference with a coverageData >= 17X There is a 0.19% of reference with a coverageData >= 18X There is a 0.18% of reference with a coverageData >= 19X There is a 0.18% of reference with a coverageData >= 20X There is a 0.18% of reference with a coverageData >= 21X There is a 0.17% of reference with a coverageData >= 22X There is a 0.17% of reference with a coverageData >= 23X There is a 0.16% of reference with a coverageData >= 24X There is a 0.16% of reference with a coverageData >= 25X There is a 0.16% of reference with a coverageData >= 26X There is a 0.16% of reference with a coverageData >= 27X There is a 0.15% of reference with a coverageData >= 28X There is a 0.15% of reference with a coverageData >= 29X There is a 0.15% of reference with a coverageData >= 30X There is a 0.14% of reference with a coverageData >= 31X There is a 0.14% of reference with a coverageData >= 32X There is a 0.14% of reference with a coverageData >= 33X There is a 0.14% of reference with a coverageData >= 34X There is a 0.14% of reference with a coverageData >= 35X There is a 0.13% of reference with a coverageData >= 36X There is a 0.13% of reference with a coverageData >= 37X There is a 0.13% of reference with a coverageData >= 38X There is a 0.13% of reference with a coverageData >= 39X There is a 0.13% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.12% of reference with a coverageData >= 42X There is a 0.12% of reference with a coverageData >= 43X There is a 0.12% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.11% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 167177051 0.6707186940168145 31.6903526049661 chr2 243199373 132335798 0.5441453091246251 47.38936698629074 chr3 198022430 150873307 0.7619000887929716 57.227754493828414 chr4 191154276 62259910 0.325705034189243 21.211577422700074 chr5 180915260 77833233 0.43021928056262365 20.17565063695344 chr6 171115067 55552326 0.3246489451451987 17.028840359755097 chr7 159138663 169874023 1.0674591566726936 45.841159421338666 chr8 146364022 65144475 0.44508530245226524 25.730744233993306 chr9 141213431 11811443 0.08364249006880939 5.631724404749926 chr10 135534747 67682985 0.4993773663074016 23.551721514193662 chr11 135006516 26264653 0.19454359521432285 13.890485475484832 chr12 133851895 102605972 0.7665634618023152 28.222006858989943 chr13 115169878 107250836 0.9312403369915874 49.96924532981583 chr14 107349540 52504764 0.4891009686674018 39.652925197070196 chr15 102531392 68507033 0.6681566656190525 30.9024956700239 chr16 90354753 128288302 1.4198290376600333 57.25950206351532 chr17 81195210 40223746 0.4953955535061736 40.18044173880671 chr18 78077248 18897505 0.24203600260091135 10.265054130762472 chr19 59128983 40176211 0.6794673096271586 21.275586471752355 chr20 63025520 92967022 1.4750694956582666 84.60092471487356 chr21 48129895 18247553 0.379131369391103 18.412014387069885 chr22 51304566 17099556 0.3332950131573085 11.716323044132727 chrMT 16571 8747 0.5278498581859876 0.9361969584780194 chrX 155270560 142191168 0.915763864057681 41.269102556292005 chrY 59373566 405608 0.006831457622067032 0.5639080849766234