BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514710.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 38,642,158 number of mapped reads = 38,403,152 (99.38%) number of supplementary alignments = 1,568,445 (4.06%) number of secondary alignments = 0 number of mapped bases = 3,702,804,250 bp number of sequenced bases = 3,700,464,628 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,280,150 duplication rate = 31.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.007 >>>>>>> ACTG content number of A's = 1,122,668,974 bp (30.34%) number of C's = 734,470,260 bp (19.85%) number of T's = 1,094,665,926 bp (29.58%) number of G's = 748,127,852 bp (20.22%) number of N's = 531,616 bp (0.01%) GC percentage = 40.07% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 20,033,007 number of insertions = 1,209,481 mapped reads with insertion percentage = 3.05% number of deletions = 1,179,768 mapped reads with deletion percentage = 2.96% homopolymer indels = 45.68% >>>>>>> Coverage mean coverageData = 1.1961X std coverageData = 42.7011X There is a 10.11% of reference with a coverageData >= 1X There is a 7.05% of reference with a coverageData >= 2X There is a 5.64% of reference with a coverageData >= 3X There is a 4.84% of reference with a coverageData >= 4X There is a 4.27% of reference with a coverageData >= 5X There is a 3.85% of reference with a coverageData >= 6X There is a 3.5% of reference with a coverageData >= 7X There is a 3.22% of reference with a coverageData >= 8X There is a 2.97% of reference with a coverageData >= 9X There is a 2.76% of reference with a coverageData >= 10X There is a 2.58% of reference with a coverageData >= 11X There is a 2.41% of reference with a coverageData >= 12X There is a 2.27% of reference with a coverageData >= 13X There is a 2.13% of reference with a coverageData >= 14X There is a 2.01% of reference with a coverageData >= 15X There is a 1.9% of reference with a coverageData >= 16X There is a 1.8% of reference with a coverageData >= 17X There is a 1.71% of reference with a coverageData >= 18X There is a 1.62% of reference with a coverageData >= 19X There is a 1.54% of reference with a coverageData >= 20X There is a 1.47% of reference with a coverageData >= 21X There is a 1.4% of reference with a coverageData >= 22X There is a 1.34% of reference with a coverageData >= 23X There is a 1.28% of reference with a coverageData >= 24X There is a 1.22% of reference with a coverageData >= 25X There is a 1.17% of reference with a coverageData >= 26X There is a 1.12% of reference with a coverageData >= 27X There is a 1.08% of reference with a coverageData >= 28X There is a 1.03% of reference with a coverageData >= 29X There is a 0.99% of reference with a coverageData >= 30X There is a 0.95% of reference with a coverageData >= 31X There is a 0.92% of reference with a coverageData >= 32X There is a 0.88% of reference with a coverageData >= 33X There is a 0.85% of reference with a coverageData >= 34X There is a 0.82% of reference with a coverageData >= 35X There is a 0.79% of reference with a coverageData >= 36X There is a 0.76% of reference with a coverageData >= 37X There is a 0.73% of reference with a coverageData >= 38X There is a 0.7% of reference with a coverageData >= 39X There is a 0.68% of reference with a coverageData >= 40X There is a 0.66% of reference with a coverageData >= 41X There is a 0.63% of reference with a coverageData >= 42X There is a 0.61% of reference with a coverageData >= 43X There is a 0.59% of reference with a coverageData >= 44X There is a 0.57% of reference with a coverageData >= 45X There is a 0.55% of reference with a coverageData >= 46X There is a 0.54% of reference with a coverageData >= 47X There is a 0.52% of reference with a coverageData >= 48X There is a 0.5% of reference with a coverageData >= 49X There is a 0.49% of reference with a coverageData >= 50X There is a 0.47% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 267864021 1.0746774468417473 11.297200545841688 chr2 243199373 402349455 1.6544016953530551 147.2956604297467 chr3 198022430 182278284 0.9204931178755861 7.30276267686567 chr4 191154276 274402000 1.4355001925251203 10.123474490569523 chr5 180915260 291701303 1.612364280381876 12.44162620920307 chr6 171115067 249120274 1.4558640473196904 10.100762633799707 chr7 159138663 235865755 1.4821398556050456 12.690960250673891 chr8 146364022 171546893 1.172056429277408 10.45799302492836 chr9 141213431 151230907 1.0709385497474386 11.471648082941613 chr10 135534747 154139941 1.137272503264421 8.581003734587094 chr11 135006516 201960609 1.4959323074450717 11.854421312465554 chr12 133851895 182511115 1.3635303033998885 15.003490054688799 chr13 115169878 93140684 0.8087243437038285 7.313908508925529 chr14 107349540 165782427 1.5443235900219041 27.831647152205647 chr15 102531392 174490609 1.7018261977756042 11.93166642715826 chr16 90354753 78235258 0.8658676539130155 7.526045745701429 chr17 81195210 51798760 0.637953396511937 5.794610990223321 chr18 78077248 69526369 0.8904818084776759 6.9794903557651615 chr19 59128983 104909234 1.7742438424824591 12.630618599379876 chr20 63025520 31727257 0.5034033356646641 5.272350349203594 chr21 48129895 43532836 0.9044864112003569 11.425068724484904 chr22 51304566 24316976 0.473972940342191 4.606983379259354 chrMT 16571 1794227 108.27511918411683 53.322802053831154 chrX 155270560 83870556 0.5401574902544307 6.172828612480889 chrY 59373566 14708500 0.24772808828763965 3.4917444850040162