BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083636.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 = 1,969,795 number of mapped reads = 1,594,462 (80.95%) number of supplementary alignments = 11,246 (0.57%) number of secondary alignments = 0 number of mapped bases = 97,731,602 bp number of sequenced bases = 97,699,538 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,625 duplication rate = 2.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0431 >>>>>>> ACTG content number of A's = 28,753,816 bp (29.43%) number of C's = 18,510,425 bp (18.95%) number of T's = 29,399,247 bp (30.09%) number of G's = 21,022,220 bp (21.52%) number of N's = 13,830 bp (0.01%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 801,697 number of insertions = 7,000 mapped reads with insertion percentage = 0.44% number of deletions = 19,836 mapped reads with deletion percentage = 1.23% homopolymer indels = 46.64% >>>>>>> Coverage mean coverageData = 0.0316X std coverageData = 0.2399X There is a 2.82% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7127778 0.028596831459850203 0.35660692322101134 chr2 243199373 8559091 0.03519372149039216 0.25667520655207005 chr3 198022430 7021908 0.035460164790422986 0.2050016375192046 chr4 191154276 6204870 0.032460011514469075 0.20125596342990074 chr5 180915260 6133952 0.03390511115535527 0.20085422516987675 chr6 171115067 5945564 0.03474599931051075 0.21352867663312933 chr7 159138663 5033440 0.031629271637150805 0.26144532517421337 chr8 146364022 5008204 0.03421745270159356 0.3515927572196683 chr9 141213431 4268839 0.0302296953609179 0.22410235837872558 chr10 135534747 4376318 0.0322892697029198 0.23807044179217968 chr11 135006516 4411924 0.03267934119565014 0.2071933014117206 chr12 133851895 4559985 0.03406739217252023 0.20229256951374888 chr13 115169878 3295623 0.028615320752532186 0.18482850865263692 chr14 107349540 3284518 0.030596479500517654 0.1957857711940435 chr15 102531392 3040808 0.029657336555032825 0.18807137016127018 chr16 90354753 2427853 0.026870230058622373 0.18941168707664796 chr17 81195210 2456429 0.030253373320913882 0.21028194247401624 chr18 78077248 2656759 0.03402731356515025 0.32278918013852076 chr19 59128983 1562983 0.02643344973479419 0.2653787108698779 chr20 63025520 1993130 0.03162417382672924 0.1972634147074822 chr21 48129895 1258368 0.026145247148367974 0.1825480392507491 chr22 51304566 974986 0.019003883591959436 0.14957934873197332 chrMT 16571 19138 1.1549091786856556 1.2634087521522332 chrX 155270560 5870135 0.03780584677481681 0.22344626674011905 chrY 59373566 238999 0.00402534353419163 0.0849956784675667