BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472593.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 = 9,569,682 number of mapped reads = 8,889,621 (92.89%) number of supplementary alignments = 283,800 (2.97%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,484,879 number of mapped paired reads (second in pair) = 4,404,742 number of mapped paired reads (both in pair) = 8,692,516 number of mapped paired reads (singletons) = 197,105 number of mapped bases = 721,840,519 bp number of sequenced bases = 721,543,032 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,424,525 duplication rate = 14.01% >>>>>>> Insert size mean insert size = 238,372.327 std insert size = 4,691,815.3131 median insert size = 126 >>>>>>> Mapping quality mean mapping quality = 50.6069 >>>>>>> ACTG content number of A's = 187,091,017 bp (25.93%) number of C's = 143,205,770 bp (19.85%) number of T's = 216,166,771 bp (29.96%) number of G's = 174,624,851 bp (24.2%) number of N's = 454,623 bp (0.06%) GC percentage = 44.05% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 8,402,801 number of insertions = 66,143 mapped reads with insertion percentage = 0.73% number of deletions = 161,167 mapped reads with deletion percentage = 1.78% homopolymer indels = 42.69% >>>>>>> Coverage mean coverageData = 0.2332X std coverageData = 2.0593X There is a 12.62% of reference with a coverageData >= 1X There is a 5.84% of reference with a coverageData >= 2X There is a 2.1% of reference with a coverageData >= 3X There is a 1.02% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 44197774 0.1773226234008059 2.581899658742393 chr2 243199373 69003591 0.2837326023862734 3.186931145599713 chr3 198022430 35214522 0.1778309760162018 0.6356416354880485 chr4 191154276 33703029 0.17631323612138292 1.0309731442544943 chr5 180915260 31708301 0.17526603891788897 0.6641726716054953 chr6 171115067 45724307 0.267213798303337 1.2078548477976636 chr7 159138663 64990067 0.4083864082733936 4.084456521739408 chr8 146364022 33895261 0.23158191840341746 1.8502898456717505 chr9 141213431 23331637 0.16522250634927213 2.1788511293905373 chr10 135534747 38077264 0.2809409752319824 2.0480948206688954 chr11 135006516 35804373 0.26520477722719693 2.0407620154901878 chr12 133851895 34554886 0.258157615176087 0.8035845725055039 chr13 115169878 32551012 0.2826347701783621 0.8498282025191548 chr14 107349540 16948372 0.15788024801969341 3.4446575838008058 chr15 102531392 19469174 0.1898850061452399 0.6813785692406793 chr16 90354753 24409481 0.27015159899778596 1.1278620498444714 chr17 81195210 21451850 0.2642009300794961 1.5990191873174868 chr18 78077248 15110257 0.1935295798335515 3.5609945281714714 chr19 59128983 11060530 0.18705767356086608 1.7939937637077281 chr20 63025520 27188197 0.43138393780804984 1.2350009022942159 chr21 48129895 10469332 0.21752243589976666 0.9344352577649331 chr22 51304566 6721035 0.13100266748187675 0.5602909312265277 chrMT 16571 206872 12.48397803391467 9.689654872355618 chrX 155270560 44360765 0.28569978107891153 1.1913151357245286 chrY 59373566 1688630 0.028440771100054864 0.7940833080734507