BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080690.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,443,228 number of mapped reads = 2,121,811 (86.84%) number of supplementary alignments = 21,862 (0.89%) number of secondary alignments = 0 number of mapped bases = 146,371,004 bp number of sequenced bases = 146,317,281 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 153,322 duplication rate = 5.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6029 >>>>>>> ACTG content number of A's = 43,088,027 bp (29.45%) number of C's = 26,518,684 bp (18.12%) number of T's = 46,856,292 bp (32.02%) number of G's = 29,852,087 bp (20.4%) number of N's = 2,191 bp (0%) GC percentage = 38.53% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,173,924 number of insertions = 11,510 mapped reads with insertion percentage = 0.54% number of deletions = 30,354 mapped reads with deletion percentage = 1.41% homopolymer indels = 48.05% >>>>>>> Coverage mean coverageData = 0.0473X std coverageData = 0.4551X There is a 3.23% of reference with a coverageData >= 1X There is a 0.98% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 11594462 0.046517284303977724 0.5195930323712282 chr2 243199373 11905211 0.048952474067439314 0.40586547089661396 chr3 198022430 10991018 0.055503904279934346 0.32239001524142585 chr4 191154276 9928440 0.05193940835516544 0.32764646955321525 chr5 180915260 9448858 0.05222808733768506 0.3127471001161204 chr6 171115067 8501619 0.04968363773600369 0.3145816109278907 chr7 159138663 8021884 0.05040813997538738 0.47942865902101145 chr8 146364022 7500592 0.0512461457228881 1.307713036955428 chr9 141213431 6177571 0.04374634166349233 0.3652561661096737 chr10 135534747 6497465 0.04793947783736963 0.3702483470527775 chr11 135006516 6828664 0.050580254955990424 0.3318090441813296 chr12 133851895 7112041 0.05313365940766098 0.3180750446912452 chr13 115169878 4811069 0.04177367453667008 0.28218764377850625 chr14 107349540 4729879 0.044060542783881516 0.29971186469017447 chr15 102531392 4016687 0.03917519231573487 0.26788152080221955 chr16 90354753 3869055 0.042820713593229566 0.29425770650321986 chr17 81195210 3070152 0.03781198422911893 0.27424260947820606 chr18 78077248 3984437 0.05103198565605181 0.5708029360300124 chr19 59128983 1996476 0.03376476135231347 0.38256454332628 chr20 63025520 2730990 0.04333149492459563 0.2872943292700127 chr21 48129895 1892671 0.039324228735591465 0.2885196022296932 chr22 51304566 1423732 0.02775059046401445 0.22029984384069282 chrMT 16571 40848 2.46502926799831 2.3655742174329246 chrX 155270560 8930859 0.057518044631255275 0.3358655687666915 chrY 59373566 366324 0.006169816379228426 0.16634111359234818