BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084802.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 = 2,023,940 number of mapped reads = 1,800,470 (88.96%) number of supplementary alignments = 19,231 (0.95%) number of secondary alignments = 0 number of mapped bases = 120,230,109 bp number of sequenced bases = 120,185,984 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,011 duplication rate = 4.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3183 >>>>>>> ACTG content number of A's = 32,668,873 bp (27.18%) number of C's = 22,332,912 bp (18.58%) number of T's = 37,996,549 bp (31.61%) number of G's = 27,170,613 bp (22.61%) number of N's = 17,037 bp (0.01%) GC percentage = 41.19% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 919,564 number of insertions = 9,093 mapped reads with insertion percentage = 0.5% number of deletions = 27,160 mapped reads with deletion percentage = 1.49% homopolymer indels = 48.29% >>>>>>> Coverage mean coverageData = 0.0388X std coverageData = 0.2645X There is a 3.22% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% 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 9323143 0.0374046931662409 0.2905226886606697 chr2 243199373 9407473 0.03868214331292705 0.4125924520545703 chr3 198022430 9601820 0.04848854748424206 0.25916231606975215 chr4 191154276 6190521 0.03238494649212032 0.215141955297918 chr5 180915260 5926946 0.032760895902313604 0.21158964579233303 chr6 171115067 10298871 0.06018681569402652 0.3059591964332206 chr7 159138663 6201268 0.03896770202222951 0.24558562202814188 chr8 146364022 5922639 0.040465128786909124 0.2594774933946095 chr9 141213431 8511796 0.060276107872487 0.31709377866662863 chr10 135534747 3879318 0.02862231336145852 0.20316227607915524 chr11 135006516 5082094 0.037643323822977554 0.24355288933261768 chr12 133851895 5230288 0.03907518828926553 0.23278148661856754 chr13 115169878 3296596 0.02862376914213628 0.19823014565906336 chr14 107349540 2291909 0.021349965728777225 0.1708316003954793 chr15 102531392 4514000 0.044025540977732945 0.2549167701195309 chr16 90354753 2227449 0.024652261514123114 0.18699337630321858 chr17 81195210 3334874 0.041072299708320235 0.23951065346930855 chr18 78077248 3517048 0.04504574751405172 0.32324486936259716 chr19 59128983 2272253 0.03842875159885635 0.2552635116038682 chr20 63025520 1832636 0.0290776815486806 0.1993781301146615 chr21 48129895 966131 0.020073407598333634 0.16680115778162913 chr22 51304566 1212313 0.023629729174592374 0.17939615764875327 chrMT 16571 21432 1.2933437933739667 1.4813325452785708 chrX 155270560 8946914 0.057621444786442454 0.28812936534350264 chrY 59373566 220377 0.0037117022750494722 0.07798298623182091