BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472780.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 = 15,298,080 number of mapped reads = 15,129,284 (98.9%) number of supplementary alignments = 51,214 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,597,589 number of mapped paired reads (second in pair) = 7,531,695 number of mapped paired reads (both in pair) = 15,029,062 number of mapped paired reads (singletons) = 100,222 number of mapped bases = 1,490,510,487 bp number of sequenced bases = 1,490,264,411 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,194,552 duplication rate = 46.59% >>>>>>> Insert size mean insert size = 26,586.8833 std insert size = 1,611,907.3217 median insert size = 256 >>>>>>> Mapping quality mean mapping quality = 55.2197 >>>>>>> ACTG content number of A's = 412,173,336 bp (27.66%) number of C's = 335,323,625 bp (22.5%) number of T's = 408,682,954 bp (27.42%) number of G's = 333,800,642 bp (22.4%) number of N's = 283,854 bp (0.02%) GC percentage = 44.9% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 9,870,127 number of insertions = 91,262 mapped reads with insertion percentage = 0.6% number of deletions = 91,509 mapped reads with deletion percentage = 0.6% homopolymer indels = 45.56% >>>>>>> Coverage mean coverageData = 0.4815X std coverageData = 15.5635X There is a 4.49% of reference with a coverageData >= 1X There is a 1.91% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 149296343 0.5989808266114611 19.690650457505477 chr2 243199373 99550141 0.4093355166668131 12.70185369480507 chr3 198022430 172941872 0.8733448630036507 20.21698232622876 chr4 191154276 53103795 0.2778059487405869 10.618816933482966 chr5 180915260 91388587 0.5051458179923574 17.398908850163888 chr6 171115067 119736468 0.6997424019943258 18.143833104577798 chr7 159138663 61478181 0.3863183203945857 11.484236941035574 chr8 146364022 73470089 0.5019682295967516 16.703731234809375 chr9 141213431 100694326 0.7130647933906513 20.137640026926963 chr10 135534747 28686942 0.2116574726036859 6.119035606835311 chr11 135006516 70421137 0.5216128753370689 20.98120282824854 chr12 133851895 78053419 0.5831327154538978 16.35521319906799 chr13 115169878 37421104 0.32492093114833376 12.795701883179863 chr14 107349540 30284129 0.2821076736798313 8.530066072409962 chr15 102531392 36095705 0.35204540088561365 11.885755562875913 chr16 90354753 43399507 0.48032345348783145 13.212577387028885 chr17 81195210 67091544 0.8262992853888794 19.652425451534018 chr18 78077248 24734669 0.3167973978795974 11.900789115267662 chr19 59128983 31686679 0.5358908168604896 15.224294492994346 chr20 63025520 28683897 0.4551155944449169 14.570501021459783 chr21 48129895 6292812 0.13074643109028183 5.523919756558421 chr22 51304566 12100514 0.23585647328153989 9.91948602752336 chrMT 16571 4179 0.252187556574739 0.7317513461906795 chrX 155270560 72093091 0.46430624710827345 17.512880360286864 chrY 59373566 1801357 0.030339376954384045 2.252907447502247