BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818819.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 = 2,612,290 number of mapped reads = 2,470,865 (94.59%) number of supplementary alignments = 18,202 (0.7%) number of secondary alignments = 0 number of mapped bases = 168,055,207 bp number of sequenced bases = 167,986,593 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,238,730 duplication rate = 41.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7726 >>>>>>> ACTG content number of A's = 49,931,161 bp (29.72%) number of C's = 34,277,613 bp (20.4%) number of T's = 46,818,494 bp (27.87%) number of G's = 36,949,106 bp (22%) number of N's = 10,219 bp (0.01%) GC percentage = 42.4% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 835,319 number of insertions = 21,827 mapped reads with insertion percentage = 0.87% number of deletions = 41,555 mapped reads with deletion percentage = 1.67% homopolymer indels = 41.33% >>>>>>> Coverage mean coverageData = 0.0543X std coverageData = 0.7023X There is a 2.28% of reference with a coverageData >= 1X There is a 1.16% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.17% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 14008746 0.05620345475488304 1.0169079701978976 chr2 243199373 14813459 0.06091076147634641 1.1884833814881737 chr3 198022430 11326869 0.057199929321138016 0.48107039867264056 chr4 191154276 11007213 0.05758287614764108 0.591425099772868 chr5 180915260 10463462 0.05783625991527746 0.5064105624349342 chr6 171115067 9815212 0.057360302468280014 0.5401054380836362 chr7 159138663 9188489 0.05773888523871788 0.5901110716297506 chr8 146364022 8621842 0.0589068398243388 0.5485556259576236 chr9 141213431 7240178 0.051271171224499174 0.5312466457779983 chr10 135534747 8242291 0.06081312122861011 0.7958335729278819 chr11 135006516 7909011 0.05858243908760671 0.5458661768173938 chr12 133851895 7675139 0.05734053298236831 0.520610154377767 chr13 115169878 5204206 0.04518721466388981 0.4195982258967182 chr14 107349540 5190702 0.04835327659531657 0.5198366056620399 chr15 102531392 4837051 0.047176293090802866 0.44194391023129614 chr16 90354753 5111479 0.05657122431622385 0.8173577240452378 chr17 81195210 4488882 0.05528505930337516 0.5060471488624979 chr18 78077248 4612801 0.059079963986435585 0.7101771867388167 chr19 59128983 3437673 0.05813854434127507 0.8523786787709686 chr20 63025520 3617550 0.05739817775402726 0.5307963749358512 chr21 48129895 2375312 0.04935211265264551 0.4805745114024134 chr22 51304566 2068907 0.040325981901883745 0.45103535524350497 chrMT 16571 88215 5.323456641120029 5.903849343553831 chrX 155270560 5054558 0.03255322837761389 0.40452657510176177 chrY 59373566 1655960 0.02789052623182512 1.3989342011282806