BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818846.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,728,711 number of mapped reads = 1,668,665 (96.53%) number of supplementary alignments = 27,973 (1.62%) number of secondary alignments = 0 number of mapped bases = 154,415,072 bp number of sequenced bases = 154,317,488 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 382,305 duplication rate = 19.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.422 >>>>>>> ACTG content number of A's = 44,125,027 bp (28.59%) number of C's = 33,192,992 bp (21.51%) number of T's = 45,234,135 bp (29.31%) number of G's = 31,763,140 bp (20.58%) number of N's = 2,194 bp (0%) GC percentage = 42.09% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 950,173 number of insertions = 21,846 mapped reads with insertion percentage = 1.26% number of deletions = 50,147 mapped reads with deletion percentage = 2.93% homopolymer indels = 40.83% >>>>>>> Coverage mean coverageData = 0.0499X std coverageData = 0.5744X There is a 3.43% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% 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 14575871 0.05847877506391448 0.8260275707999523 chr2 243199373 11716046 0.048174655450283585 0.8188863041298865 chr3 198022430 9636851 0.048665451686457945 0.30063165032230277 chr4 191154276 7873147 0.041187396718240295 0.36658761565679715 chr5 180915260 6832900 0.037768511069768244 0.27602143826698367 chr6 171115067 7678432 0.04487291583738795 0.3139641927045667 chr7 159138663 13832408 0.08692047387629491 1.2097284143245672 chr8 146364022 13387910 0.09146995154314631 0.5141230751556184 chr9 141213431 5755106 0.04075466447663891 0.48972383619589205 chr10 135534747 7206803 0.05317310254026593 0.7891837794700526 chr11 135006516 6864093 0.05084267932667783 0.36144099990527356 chr12 133851895 6085175 0.04546200111698082 0.29154443250617984 chr13 115169878 4756342 0.041298489523449874 0.2701415715423953 chr14 107349540 4517130 0.04207870848817796 0.2997574078643752 chr15 102531392 4187137 0.040837610007284406 0.27047517968031076 chr16 90354753 3811205 0.0421804595049914 0.5845352870228018 chr17 81195210 3811207 0.04693881572570599 0.37645212828208796 chr18 78077248 2999481 0.038416838154951366 0.566455819400143 chr19 59128983 2638230 0.04461822047573522 0.6992557209279817 chr20 63025520 6367644 0.10103278798810386 0.46103399514762505 chr21 48129895 1401964 0.029128756669841063 0.2820976586167552 chr22 51304566 1398025 0.027249523950753234 0.24682922044381772 chrMT 16571 261024 15.75185565143926 10.150159177783 chrX 155270560 6239580 0.04018520961088824 0.31857002423811137 chrY 59373566 581361 0.009791579640003432 0.7167916947510165