BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472754.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 = 21,612,772 number of mapped reads = 21,441,385 (99.21%) number of supplementary alignments = 72,793 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,753,840 number of mapped paired reads (second in pair) = 10,687,545 number of mapped paired reads (both in pair) = 21,333,710 number of mapped paired reads (singletons) = 107,675 number of mapped bases = 2,111,227,961 bp number of sequenced bases = 2,110,929,508 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,277,638 duplication rate = 49.14% >>>>>>> Insert size mean insert size = 26,142.6044 std insert size = 1,630,538.9905 median insert size = 238 >>>>>>> Mapping quality mean mapping quality = 55.2305 >>>>>>> ACTG content number of A's = 574,054,722 bp (27.19%) number of C's = 484,561,366 bp (22.95%) number of T's = 570,388,109 bp (27.02%) number of G's = 481,511,666 bp (22.81%) number of N's = 413,645 bp (0.02%) GC percentage = 45.77% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 12,581,449 number of insertions = 126,671 mapped reads with insertion percentage = 0.58% number of deletions = 120,061 mapped reads with deletion percentage = 0.55% homopolymer indels = 45.32% >>>>>>> Coverage mean coverageData = 0.682X std coverageData = 23.7072X There is a 5.76% of reference with a coverageData >= 1X There is a 2.62% of reference with a coverageData >= 2X There is a 1.17% of reference with a coverageData >= 3X There is a 0.81% of reference with a coverageData >= 4X There is a 0.58% of reference with a coverageData >= 5X There is a 0.51% of reference with a coverageData >= 6X There is a 0.45% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.3% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.22% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 257901302 1.0347067580626008 36.03696275125091 chr2 243199373 155438128 0.6391386872531123 23.088654339864263 chr3 198022430 227196750 1.1473283607316604 28.073680975330454 chr4 191154276 85981917 0.4498037857128553 19.682626439668805 chr5 180915260 93284159 0.5156234968791467 17.008560044281484 chr6 171115067 128350249 0.7500815167842584 25.428432141445246 chr7 159138663 107214037 0.6737145768278825 20.287841581148744 chr8 146364022 87468077 0.597606404940143 24.215739674716453 chr9 141213431 138369744 0.9798624891424103 25.310437727741174 chr10 135534747 79035188 0.5831359835717995 24.376764599116644 chr11 135006516 102861867 0.7619029810383374 28.651766437265373 chr12 133851895 106101661 0.7926795582535459 22.297520662698485 chr13 115169878 37136498 0.32244974679924554 14.093654402444711 chr14 107349540 56945422 0.5304673126685033 27.16032850514156 chr15 102531392 53912390 0.5258134991476562 18.510917219449155 chr16 90354753 76273569 0.844156687584548 23.07669830033543 chr17 81195210 73134311 0.9007219884030104 19.73513243657467 chr18 78077248 40767440 0.5221423787887606 29.37224546797131 chr19 59128983 28975591 0.4900404087788894 13.662281103262664 chr20 63025520 42480898 0.6740269338515573 16.952157123921204 chr21 48129895 8495140 0.17650443658769668 6.774839295883462 chr22 51304566 22308583 0.43482646359390315 11.371568957865083 chrMT 16571 2419 0.14597791322189366 0.4938753135075201 chrX 155270560 96533594 0.6217121520009975 21.297855028617963 chrY 59373566 5059027 0.08520672314005866 3.7361717104800953