BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472666.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 = 16,688,888 number of mapped reads = 16,489,450 (98.8%) number of supplementary alignments = 93,530 (0.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,277,578 number of mapped paired reads (second in pair) = 8,211,872 number of mapped paired reads (both in pair) = 16,363,670 number of mapped paired reads (singletons) = 125,780 number of mapped bases = 1,618,510,994 bp number of sequenced bases = 1,618,277,760 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,388,343 duplication rate = 49.71% >>>>>>> Insert size mean insert size = 24,706.3258 std insert size = 1,539,790.0873 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 54.9681 >>>>>>> ACTG content number of A's = 432,298,767 bp (26.71%) number of C's = 378,769,390 bp (23.41%) number of T's = 432,567,103 bp (26.73%) number of G's = 374,326,107 bp (23.13%) number of N's = 316,393 bp (0.02%) GC percentage = 46.54% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 10,032,500 number of insertions = 101,693 mapped reads with insertion percentage = 0.61% number of deletions = 92,302 mapped reads with deletion percentage = 0.55% homopolymer indels = 44.49% >>>>>>> Coverage mean coverageData = 0.5228X std coverageData = 22.5843X There is a 3.27% of reference with a coverageData >= 1X There is a 1.55% of reference with a coverageData >= 2X There is a 0.74% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 157760512 0.6329392936597739 23.03518217048444 chr2 243199373 176831969 0.7271070102635503 36.86725533015542 chr3 198022430 163805760 0.827208109707572 24.11805293137143 chr4 191154276 36806507 0.19254869820437603 11.506568147683666 chr5 180915260 64495167 0.35649379162376904 20.41025081906529 chr6 171115067 117508329 0.6867211114729015 21.14016422074052 chr7 159138663 93323803 0.586430734308733 23.279646378549028 chr8 146364022 74710472 0.5104428737275339 19.28304164543731 chr9 141213431 87635548 0.6205893262376722 22.59746252140612 chr10 135534747 44073277 0.32518064906263483 16.641334512343512 chr11 135006516 45525152 0.3372070722867924 15.680602354944305 chr12 133851895 59053982 0.4411889872758245 17.39195578277156 chr13 115169878 62326841 0.5411731095174035 31.600159499284217 chr14 107349540 21099277 0.19654743746456668 10.269521852476133 chr15 102531392 24419321 0.23816433702567893 12.70698872565959 chr16 90354753 107408306 1.1887399658986395 43.36466693847757 chr17 81195210 38584812 0.47521044652757227 14.121914731024484 chr18 78077248 9782541 0.12529310715459643 6.06835444748356 chr19 59128983 28978267 0.4900856657724013 12.323042585853855 chr20 63025520 68405453 1.0853611838506052 29.565265739947147 chr21 48129895 9881577 0.20531058711015265 13.438103995798434 chr22 51304566 27257896 0.5312957135238217 21.01827778441425 chrMT 16571 4574 0.27602437994086054 0.7446818057817177 chrX 155270560 97899173 0.630506987287223 21.57045285892254 chrY 59373566 932478 0.015705271938694063 1.2819555867689352