BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708537.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 21,326,306 number of mapped reads = 20,834,384 (97.69%) number of supplementary alignments = 541 (0%) number of secondary alignments = 0 number of mapped bases = 1,039,142,908 bp number of sequenced bases = 1,039,051,946 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 221,055 duplication rate = 1.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6571 >>>>>>> ACTG content number of A's = 320,356,001 bp (30.83%) number of C's = 197,081,787 bp (18.97%) number of T's = 320,639,035 bp (30.86%) number of G's = 200,938,443 bp (19.34%) number of N's = 36,680 bp (0%) GC percentage = 38.31% >>>>>>> Mismatches and indels general error rate = 0.002 number of mismatches = 2,033,004 number of insertions = 61,038 mapped reads with insertion percentage = 0.29% number of deletions = 55,180 mapped reads with deletion percentage = 0.26% homopolymer indels = 49.37% >>>>>>> Coverage mean coverageData = 0.3357X std coverageData = 0.6678X There is a 25.26% of reference with a coverageData >= 1X There is a 6.27% of reference with a coverageData >= 2X There is a 1.52% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.03% 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 78980407 0.3168714552570764 0.6617236207613882 chr2 243199373 94002355 0.38652383778966404 0.7046367142547435 chr3 198022430 86697320 0.4378156555295276 0.7543436368394197 chr4 191154276 82147542 0.4297447261917384 0.7388551862040189 chr5 180915260 71467510 0.3950330668623531 0.7102516264926798 chr6 171115067 73983618 0.43236179780708617 0.7520115694702093 chr7 159138663 58202123 0.36573213512545344 0.6932851323261798 chr8 146364022 56144899 0.38359767812338474 0.6984101562871218 chr9 141213431 42788366 0.3030049315918115 0.6426660025526685 chr10 135534747 44615930 0.32918444153660464 0.6477943962138444 chr11 135006516 48706874 0.36077424588899104 0.6957148214055947 chr12 133851895 47771224 0.35689613509020546 0.6864198221019099 chr13 115169878 39603886 0.343873647239602 0.6753717132692835 chr14 107349540 32392229 0.30174539173619186 0.6367119001441869 chr15 102531392 27804468 0.271180049910958 0.6089126662342984 chr16 90354753 19545032 0.21631437584694632 0.5326028502031074 chr17 81195210 17798950 0.2192118229634482 0.5348384800960077 chr18 78077248 30391572 0.38925004118997636 0.7063650285157865 chr19 59128983 8953325 0.1514202434362857 0.4373862156653559 chr20 63025520 16916780 0.2684115894640774 0.5962329262108936 chr21 48129895 12939838 0.26885240451906245 0.6150395746129488 chr22 51304566 5787944 0.11281537787494392 0.3834875015781119 chrMT 16571 797 0.04809607145012371 0.22895620120612836 chrX 155270560 36416839 0.2345379510449373 0.5365090245882085 chrY 59373566 5083080 0.0856118360820706 0.34034415246439487