BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081944.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 = 3,083,169 number of mapped reads = 2,826,708 (91.68%) number of supplementary alignments = 17,746 (0.58%) number of secondary alignments = 0 number of mapped bases = 191,847,944 bp number of sequenced bases = 191,775,409 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 146,310 duplication rate = 3.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1108 >>>>>>> ACTG content number of A's = 54,009,570 bp (28.16%) number of C's = 35,437,457 bp (18.48%) number of T's = 60,367,067 bp (31.48%) number of G's = 41,936,957 bp (21.87%) number of N's = 24,358 bp (0.01%) GC percentage = 40.35% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,490,125 number of insertions = 14,416 mapped reads with insertion percentage = 0.51% number of deletions = 40,682 mapped reads with deletion percentage = 1.43% homopolymer indels = 47.84% >>>>>>> Coverage mean coverageData = 0.062X std coverageData = 0.5923X There is a 5.22% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.11% 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 0.01% 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 17466119 0.07007452551141287 1.0133315410051442 chr2 243199373 16665372 0.06852555495692006 0.8982947366840568 chr3 198022430 11735936 0.05926569025539177 0.2797447515428847 chr4 191154276 9867637 0.05162132496580929 0.30530797235783197 chr5 180915260 10718144 0.059244001860318474 0.28021042267667606 chr6 171115067 16658730 0.09735396357586676 0.46581991289817837 chr7 159138663 12500084 0.07854837890651375 0.8020231297177689 chr8 146364022 10694354 0.07306682239163939 0.8238396203650172 chr9 141213431 11278439 0.07986803323261794 0.6734126698095904 chr10 135534747 7618310 0.056209275987359905 0.58760258557014 chr11 135006516 8436018 0.06248600623098814 0.43050944671816216 chr12 133851895 7834116 0.058528241232595174 0.30050710265428976 chr13 115169878 5017492 0.04356600950814587 0.23673743833396466 chr14 107349540 3661499 0.0341081945949652 0.2845947605473983 chr15 102531392 4157536 0.04054890818218873 0.23093948916705487 chr16 90354753 4125327 0.04565700046792226 0.33149172376106645 chr17 81195210 6228661 0.07671217304567597 0.3748622701334264 chr18 78077248 5803680 0.07433253795010808 1.0170050545352738 chr19 59128983 2943103 0.049774287509731056 0.8143477274440574 chr20 63025520 4700673 0.07458364484735706 0.3255541813987203 chr21 48129895 2053468 0.042665125282321935 0.2978032369661026 chr22 51304566 1502365 0.029283261064911845 0.1910418779433608 chrMT 16571 21818 1.3166374992456702 1.3728329040104967 chrX 155270560 9654740 0.062180106776197626 0.36680433613418645 chrY 59373566 504323 0.008494066197741937 0.22563116285371584