BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818999.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 973,888 number of mapped reads = 949,332 (97.48%) number of supplementary alignments = 15,831 (1.63%) number of secondary alignments = 0 number of mapped bases = 87,628,979 bp number of sequenced bases = 87,572,899 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 232,356 duplication rate = 21.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0399 >>>>>>> ACTG content number of A's = 25,661,777 bp (29.3%) number of C's = 17,888,529 bp (20.43%) number of T's = 24,901,740 bp (28.44%) number of G's = 19,116,513 bp (21.83%) number of N's = 4,340 bp (0%) GC percentage = 42.26% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 589,200 number of insertions = 15,493 mapped reads with insertion percentage = 1.59% number of deletions = 29,836 mapped reads with deletion percentage = 3.07% homopolymer indels = 39.71% >>>>>>> Coverage mean coverageData = 0.0283X std coverageData = 0.403X There is a 1.94% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 8554486 0.03432082121071225 0.7850651460611123 chr2 243199373 7175147 0.02950314760885506 0.5506460325791589 chr3 198022430 4689598 0.023682155602271923 0.20975341839113817 chr4 191154276 5069740 0.02652171903285072 0.28482779220189125 chr5 180915260 4671021 0.02581883363515051 0.22633550798930835 chr6 171115067 3594274 0.0210050117912761 0.2296134130968816 chr7 159138663 4340823 0.02727698548026635 0.4018589844472809 chr8 146364022 8027327 0.05484494679983582 0.3597887645150974 chr9 141213431 3718208 0.026330413287670915 0.3289037268383839 chr10 135534747 4877750 0.035988926146001514 0.5688640618702085 chr11 135006516 2884056 0.021362346688510947 0.2443478444127773 chr12 133851895 3961445 0.029595733403699663 0.23796964714799998 chr13 115169878 1953103 0.016958453320580925 0.17591078109220756 chr14 107349540 2006217 0.018688640864227272 0.19940672452414285 chr15 102531392 2277648 0.022214152715297183 0.2013594032722292 chr16 90354753 2822498 0.031237958228937886 0.4475226751289032 chr17 81195210 2984597 0.036758289066559466 0.299880566292617 chr18 78077248 2091687 0.026789968314456986 0.41374642382072463 chr19 59128983 1803093 0.03049423325951674 0.6521014306528395 chr20 63025520 2555470 0.04054659128556178 0.2945434288399395 chr21 48129895 1201492 0.024963528385008944 0.24725067585236135 chr22 51304566 669867 0.013056674136956933 0.16758926207507924 chrMT 16571 17636 1.0642689035061252 1.7055805908859578 chrX 155270560 5268110 0.0339285824692073 0.3116580060517806 chrY 59373566 413686 0.006967511434297209 0.4569926720703018