BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089706.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 8,149,283 number of mapped reads = 6,073,263 (74.53%) number of supplementary alignments = 438 (0.01%) number of secondary alignments = 0 number of mapped bases = 286,729,992 bp number of sequenced bases = 286,675,660 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,615,316 duplication rate = 15.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1602 >>>>>>> ACTG content number of A's = 78,397,022 bp (27.35%) number of C's = 61,988,746 bp (21.62%) number of T's = 79,685,724 bp (27.8%) number of G's = 66,596,382 bp (23.23%) number of N's = 7,786 bp (0%) GC percentage = 44.85% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 1,476,005 number of insertions = 11,278 mapped reads with insertion percentage = 0.19% number of deletions = 36,184 mapped reads with deletion percentage = 0.59% homopolymer indels = 46.19% >>>>>>> Coverage mean coverageData = 0.0926X std coverageData = 0.685X There is a 4.9% of reference with a coverageData >= 1X There is a 1.77% of reference with a coverageData >= 2X There is a 0.87% of reference with a coverageData >= 3X There is a 0.49% of reference with a coverageData >= 4X There is a 0.31% of reference with a coverageData >= 5X There is a 0.21% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 22863074 0.09172724989920887 0.9186582066167951 chr2 243199373 24165148 0.0993635291979145 0.7089459589917488 chr3 198022430 18798728 0.09493231650576149 0.6051554302357243 chr4 191154276 17063858 0.08926746687058154 0.5955405493426997 chr5 180915260 16959100 0.09374057224360179 0.6043160596399554 chr6 171115067 16545428 0.09669182433829746 0.6793878246271108 chr7 159138663 15621942 0.09816559788490871 0.7694614484723595 chr8 146364022 14159470 0.0967414656041633 0.647952832759501 chr9 141213431 12060598 0.08540687606407638 0.640965401397221 chr10 135534747 14113758 0.10413387203209226 0.7201276316739725 chr11 135006516 12801122 0.0948185493506106 0.6686717748981421 chr12 133851895 12820965 0.09578471040697631 0.6246107788127997 chr13 115169878 9021227 0.07832974347684904 0.5575960541321341 chr14 107349540 8799366 0.08196929395319254 0.56580252226785 chr15 102531392 8313443 0.08108192854730774 0.5584263386980197 chr16 90354753 9297233 0.102896999784837 0.6596049723801057 chr17 81195210 8863209 0.10915925951789521 0.6732303387102783 chr18 78077248 7339259 0.09399997038830057 1.0456593788613486 chr19 59128983 6384337 0.10797305612376253 0.7937456947408907 chr20 63025520 6546631 0.10387270108997117 0.6975911655078935 chr21 48129895 3698655 0.07684735235761474 0.5780079573186087 chr22 51304566 3883845 0.07570174163445803 0.5610187053653142 chrMT 16571 86969 5.248265041337276 5.32499466455698 chrX 155270560 15705403 0.10114862083320882 0.6658142798823415 chrY 59373566 817224 0.013764105056448858 0.26166048201515274