BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617653.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,226,293 (94.46%) number of supplementary alignments = 158,842 (0.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,230,238 number of mapped paired reads (second in pair) = 14,996,055 number of mapped paired reads (both in pair) = 29,580,764 number of mapped paired reads (singletons) = 645,529 number of mapped bases = 2,926,534,537 bp number of sequenced bases = 2,924,760,548 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,949,475 duplication rate = 10.79% >>>>>>> Insert size mean insert size = 40,885.7858 std insert size = 1,880,251.2676 median insert size = 225 >>>>>>> Mapping quality mean mapping quality = 52.5833 >>>>>>> ACTG content number of A's = 869,649,148 bp (29.73%) number of C's = 582,120,056 bp (19.9%) number of T's = 869,525,115 bp (29.73%) number of G's = 599,779,761 bp (20.51%) number of N's = 3,686,468 bp (0.13%) GC percentage = 40.41% >>>>>>> Mismatches and indels general error rate = 0.0159 number of mismatches = 45,598,898 number of insertions = 458,255 mapped reads with insertion percentage = 1.49% number of deletions = 1,072,346 mapped reads with deletion percentage = 3.47% homopolymer indels = 47.5% >>>>>>> Coverage mean coverageData = 0.9454X std coverageData = 10.4183X There is a 33.27% of reference with a coverageData >= 1X There is a 19.25% of reference with a coverageData >= 2X There is a 11.75% of reference with a coverageData >= 3X There is a 7.5% of reference with a coverageData >= 4X There is a 4.93% of reference with a coverageData >= 5X There is a 3.34% of reference with a coverageData >= 6X There is a 2.31% of reference with a coverageData >= 7X There is a 1.64% of reference with a coverageData >= 8X There is a 1.19% of reference with a coverageData >= 9X There is a 0.88% of reference with a coverageData >= 10X There is a 0.66% of reference with a coverageData >= 11X There is a 0.5% of reference with a coverageData >= 12X There is a 0.39% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 179687444 0.720910717410008 10.090202141230716 chr2 243199373 301781066 1.240879292891927 11.996434673539806 chr3 198022430 245437897 1.2394449305566042 2.481928649207723 chr4 191154276 163679373 0.8562684362865103 8.164686971674275 chr5 180915260 193800697 1.0712236049076236 2.327077916898952 chr6 171115067 141962617 0.8296324776590246 5.8048910139932515 chr7 159138663 228613432 1.43656750465473 13.291944968508233 chr8 146364022 130172155 0.8893726287461545 4.059343615847822 chr9 141213431 119619256 0.8470812949796539 19.742641859368863 chr10 135534747 124117014 0.9157578904839805 21.216797382480383 chr11 135006516 161001800 1.1925483655914801 11.786034740039431 chr12 133851895 125199148 0.9353558124821468 2.171480195501145 chr13 115169878 125725179 1.091649840941917 2.298899837141204 chr14 107349540 83811651 0.7807360050168822 2.4547972829698295 chr15 102531392 62430490 0.6088914700387565 1.6531834796704745 chr16 90354753 81258081 0.8993227063550271 16.63395623159174 chr17 81195210 72141215 0.8884910205909929 12.524886789816222 chr18 78077248 53765156 0.6886148958528866 17.994446565703765 chr19 59128983 31049950 0.5251223414412522 6.037194140372543 chr20 63025520 79130439 1.2555301249398656 3.0187909727486044 chr21 48129895 42709736 0.8873847740577867 4.338950473807849 chr22 51304566 18871931 0.3678411586212424 1.2680558189106976 chrMT 16571 3149678 190.07169150926316 130.9136749755464 chrX 155270560 145794695 0.9389719145728591 4.317610262899686 chrY 59373566 11624437 0.1957847200890713 16.780443594778852