BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818857.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 = 1,421,835 number of mapped reads = 1,392,941 (97.97%) number of supplementary alignments = 22,206 (1.56%) number of secondary alignments = 0 number of mapped bases = 128,811,926 bp number of sequenced bases = 128,729,201 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 293,514 duplication rate = 17.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3904 >>>>>>> ACTG content number of A's = 36,623,631 bp (28.45%) number of C's = 27,914,325 bp (21.68%) number of T's = 36,323,861 bp (28.22%) number of G's = 27,865,608 bp (21.65%) number of N's = 1,776 bp (0%) GC percentage = 43.33% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 783,554 number of insertions = 16,209 mapped reads with insertion percentage = 1.12% number of deletions = 41,610 mapped reads with deletion percentage = 2.91% homopolymer indels = 40.5% >>>>>>> Coverage mean coverageData = 0.0416X std coverageData = 0.5175X There is a 2.96% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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 12296842 0.04933525120485056 0.7880913176440041 chr2 243199373 9727107 0.039996431240799296 0.7892204289901206 chr3 198022430 7730160 0.03903678992324253 0.2580532370739428 chr4 191154276 6598682 0.03452019038276706 0.3259830961197682 chr5 180915260 7350979 0.040632166684004434 0.2776253898672878 chr6 171115067 6377036 0.037267530626043585 0.2735837391093232 chr7 159138663 11612671 0.07297202817394538 1.0248790554696678 chr8 146364022 10605518 0.07245986995356003 0.440675270549466 chr9 141213431 3710625 0.026276714429521935 0.3925695720152839 chr10 135534747 5029539 0.03710885297922901 0.6757810777037484 chr11 135006516 5721674 0.042380724794053644 0.323229226323063 chr12 133851895 5099945 0.03810140304700206 0.2599882164795227 chr13 115169878 3055263 0.02652831671836971 0.20920977975929778 chr14 107349540 4143362 0.03859692365705526 0.27628596559588237 chr15 102531392 3633397 0.03543692257684359 0.24805771580578706 chr16 90354753 3325490 0.03680481534823077 0.5535958869289637 chr17 81195210 3336836 0.04109646369533375 0.33820971440541103 chr18 78077248 2345829 0.030044975458151393 0.46816313844035157 chr19 59128983 2565556 0.04338914471097871 0.7150873155804115 chr20 63025520 5406930 0.0857895341442641 0.41198645002362483 chr21 48129895 1650222 0.034286839811306466 0.29142589641771 chr22 51304566 1593336 0.031056417083812776 0.25548857905204875 chrMT 16571 175877 10.613541729527487 7.063330279848079 chrX 155270560 5210561 0.03355794556289357 0.2897112420476716 chrY 59373566 508489 0.008564232102885651 0.603753069902316