BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080978.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 = 4,827,360 number of mapped reads = 4,086,883 (84.66%) number of supplementary alignments = 38,847 (0.8%) number of secondary alignments = 0 number of mapped bases = 273,787,039 bp number of sequenced bases = 273,688,347 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 302,566 duplication rate = 5.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0287 >>>>>>> ACTG content number of A's = 76,624,888 bp (28%) number of C's = 47,857,636 bp (17.49%) number of T's = 89,608,935 bp (32.74%) number of G's = 59,054,608 bp (21.58%) number of N's = 542,280 bp (0.2%) GC percentage = 39.06% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 2,729,663 number of insertions = 21,742 mapped reads with insertion percentage = 0.53% number of deletions = 59,617 mapped reads with deletion percentage = 1.44% homopolymer indels = 49.57% >>>>>>> Coverage mean coverageData = 0.0884X std coverageData = 0.6386X There is a 6.26% of reference with a coverageData >= 1X There is a 1.7% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% 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 0.01% 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 22489463 0.09022831281130489 0.9260156749083617 chr2 243199373 18183388 0.07476741315447388 0.559648547623083 chr3 198022430 24438370 0.12341213063590827 0.4697764289022928 chr4 191154276 17292089 0.09046142917566752 0.418233421235469 chr5 180915260 15906671 0.08792332388102585 0.39400718606005547 chr6 171115067 23355061 0.13648746080320326 0.7224390720827186 chr7 159138663 13507696 0.08488003949109463 0.6398276295849704 chr8 146364022 21049999 0.1438194900110083 1.3004876045962126 chr9 141213431 14154043 0.10023156366762309 0.7544949989921382 chr10 135534747 12260083 0.09045712093298112 0.516927669959704 chr11 135006516 12203858 0.09039458510284051 0.512913299002011 chr12 133851895 13492199 0.10079946197250327 0.43309876157643434 chr13 115169878 7660662 0.06651619445146933 0.33809539012662027 chr14 107349540 7656965 0.07132741323344283 0.41738420306284396 chr15 102531392 6722751 0.0655677336361531 0.33495348189896074 chr16 90354753 5976997 0.06615033301015166 0.416044383275795 chr17 81195210 5081243 0.06258057587387236 0.34485443477497096 chr18 78077248 6670363 0.08543286515426364 1.328345096526398 chr19 59128983 5089061 0.08606711534341796 0.7062285656011116 chr20 63025520 4350614 0.06902940269275049 0.3665035348177974 chr21 48129895 5070014 0.10534022565393089 0.5053353621776595 chr22 51304566 2254950 0.04395222834552387 0.26839550991585265 chrMT 16571 263982 15.930360267937964 7.8587551836660445 chrX 155270560 8062357 0.05192456960289188 0.3390074448431909 chrY 59373566 594160 0.010007146951557534 0.20068926859935615