BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472496.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 = 20,700,968 number of mapped reads = 20,449,760 (98.79%) number of supplementary alignments = 69,790 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,254,771 number of mapped paired reads (second in pair) = 10,194,989 number of mapped paired reads (both in pair) = 20,324,882 number of mapped paired reads (singletons) = 124,878 number of mapped bases = 2,009,820,267 bp number of sequenced bases = 2,009,563,191 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,290,181 duplication rate = 46.87% >>>>>>> Insert size mean insert size = 27,852.5505 std insert size = 1,655,912.7972 median insert size = 236 >>>>>>> Mapping quality mean mapping quality = 55.1427 >>>>>>> ACTG content number of A's = 550,981,020 bp (27.42%) number of C's = 457,508,800 bp (22.77%) number of T's = 546,792,478 bp (27.21%) number of G's = 453,969,957 bp (22.59%) number of N's = 310,936 bp (0.02%) GC percentage = 45.36% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 12,160,532 number of insertions = 109,082 mapped reads with insertion percentage = 0.53% number of deletions = 102,795 mapped reads with deletion percentage = 0.5% homopolymer indels = 45.13% >>>>>>> Coverage mean coverageData = 0.6492X std coverageData = 23.21X There is a 6.31% of reference with a coverageData >= 1X There is a 2.9% of reference with a coverageData >= 2X There is a 1.25% of reference with a coverageData >= 3X There is a 0.85% of reference with a coverageData >= 4X There is a 0.58% of reference with a coverageData >= 5X There is a 0.5% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 216811746 0.8698543864410272 30.639300650504506 chr2 243199373 167071306 0.686972601693344 22.22212161452713 chr3 198022430 200433628 1.0121763883010626 21.70494943037657 chr4 191154276 85625771 0.4479406518743007 15.064161866622422 chr5 180915260 116984975 0.6466285652188765 20.06628354782483 chr6 171115067 115878926 0.6771988465516015 19.78672421719679 chr7 159138663 70090101 0.44043414515805 15.082751787743137 chr8 146364022 99987963 0.6831457733513226 31.632599378689374 chr9 141213431 109970953 0.7787570362198762 20.57513032750197 chr10 135534747 65143935 0.4806437938752341 20.453326918371676 chr11 135006516 76800038 0.5688617133116746 22.74136766205201 chr12 133851895 114807895 0.8577233441483962 36.57416245660319 chr13 115169878 43003999 0.3733962364707897 13.880544885550734 chr14 107349540 48763935 0.4542537862761219 18.978033747332706 chr15 102531392 40650058 0.39646450913296877 11.346376807565806 chr16 90354753 76387531 0.8454179604696612 33.85630791014016 chr17 81195210 79369490 0.9775144371201208 24.144168363026917 chr18 78077248 30727849 0.3935570193252713 13.645462799408412 chr19 59128983 56905444 0.9623951083346047 44.549443871408656 chr20 63025520 33468707 0.5310342064611288 14.120681486308202 chr21 48129895 7996607 0.16614636287903806 6.478227892237348 chr22 51304566 21863097 0.42614329882451396 11.945232281483992 chrMT 16571 2048 0.12358940317422003 0.41258993802673793 chrX 155270560 125554033 0.808614543542575 26.487562772217068 chrY 59373566 5520232 0.09297457390381436 4.537965368294534