BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082926.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 = 1,876,825 number of mapped reads = 1,690,990 (90.1%) number of supplementary alignments = 18,830 (1%) number of secondary alignments = 0 number of mapped bases = 113,009,116 bp number of sequenced bases = 112,967,256 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,351 duplication rate = 4.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5922 >>>>>>> ACTG content number of A's = 30,756,630 bp (27.23%) number of C's = 21,389,979 bp (18.93%) number of T's = 35,253,881 bp (31.21%) number of G's = 25,561,756 bp (22.63%) number of N's = 5,010 bp (0%) GC percentage = 41.56% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 798,516 number of insertions = 8,641 mapped reads with insertion percentage = 0.51% number of deletions = 25,687 mapped reads with deletion percentage = 1.51% homopolymer indels = 48.49% >>>>>>> Coverage mean coverageData = 0.0365X std coverageData = 0.2661X There is a 3% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 10125268 0.04062283961170151 0.3017420861093726 chr2 243199373 10184007 0.04187513674223165 0.3918903643747122 chr3 198022430 7709548 0.0389327007046626 0.23270847829218436 chr4 191154276 6280323 0.03285473457052041 0.21829001053409583 chr5 180915260 5978777 0.03304738914782534 0.21454764660203424 chr6 171115067 8059197 0.04709811439339821 0.30212691658902907 chr7 159138663 5155317 0.03239512575269028 0.24480305025156415 chr8 146364022 11503645 0.07859612521443282 0.37567865288946417 chr9 141213431 3022933 0.02140683771078404 0.21152185629569617 chr10 135534747 3753833 0.02769646222160285 0.20823423113812076 chr11 135006516 4961265 0.03674833739135969 0.2516442820476417 chr12 133851895 3670905 0.02742512535963723 0.19550107382143153 chr13 115169878 2984403 0.025913051674848524 0.1906276401335331 chr14 107349540 2314879 0.02156393963122711 0.1830554032933043 chr15 102531392 2022408 0.019724768781057805 0.17279329423340276 chr16 90354753 4775455 0.052852283266160885 0.27839972408878605 chr17 81195210 3429552 0.04223835371569333 0.2518653379833325 chr18 78077248 3617688 0.04633472737153851 0.4161663630094119 chr19 59128983 1422046 0.02404989783098417 0.22963525593561268 chr20 63025520 2818371 0.04471793330701595 0.2576970118331475 chr21 48129895 2505223 0.052051287458657454 0.27408493026555064 chr22 51304566 1358645 0.02648195094370353 0.19322585832204658 chrMT 16571 147686 8.912316697845634 5.558945488866586 chrX 155270560 5016858 0.03231042639377355 0.2182566318390039 chrY 59373566 190884 0.003214966067559425 0.06722459485226107