BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514723.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 72,535,785 number of mapped reads = 72,000,368 (99.26%) number of supplementary alignments = 5,055,737 (6.97%) number of secondary alignments = 0 number of mapped bases = 6,878,932,447 bp number of sequenced bases = 6,875,122,845 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,002,285 duplication rate = 49.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5651 >>>>>>> ACTG content number of A's = 1,973,276,334 bp (28.7%) number of C's = 1,454,106,867 bp (21.15%) number of T's = 1,960,962,033 bp (28.52%) number of G's = 1,482,889,218 bp (21.57%) number of N's = 3,888,393 bp (0.06%) GC percentage = 42.72% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 48,095,928 number of insertions = 2,927,166 mapped reads with insertion percentage = 3.97% number of deletions = 1,934,088 mapped reads with deletion percentage = 2.62% homopolymer indels = 47.07% >>>>>>> Coverage mean coverageData = 2.2221X std coverageData = 187.3391X There is a 3.83% of reference with a coverageData >= 1X There is a 1.68% of reference with a coverageData >= 2X There is a 1% of reference with a coverageData >= 3X There is a 0.75% of reference with a coverageData >= 4X There is a 0.61% of reference with a coverageData >= 5X There is a 0.53% of reference with a coverageData >= 6X There is a 0.48% of reference with a coverageData >= 7X There is a 0.44% of reference with a coverageData >= 8X There is a 0.42% of reference with a coverageData >= 9X There is a 0.39% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 537852625 2.1578787761575926 229.80063124108833 chr2 243199373 654755941 2.6922599878577813 342.4558415483177 chr3 198022430 523508365 2.643682157622245 163.20352709048498 chr4 191154276 565155366 2.9565405379684 205.17043391349873 chr5 180915260 298119061 1.6478381149273975 89.48640228885108 chr6 171115067 214506622 1.2535811472405292 66.79853299616866 chr7 159138663 472530737 2.969301916279138 136.20066590534861 chr8 146364022 508024765 3.470967510034672 256.0459335623197 chr9 141213431 190063406 1.3459300907432807 66.4633343340624 chr10 135534747 221131117 1.6315455770172353 100.36035701759195 chr11 135006516 343127314 2.5415611347233047 167.50952905925027 chr12 133851895 271009811 2.0246990974614145 114.06140295783702 chr13 115169878 182189101 1.5819162454960662 78.26103668835263 chr14 107349540 139451348 1.2990400145170626 80.93044987702469 chr15 102531392 241184628 2.3523003374420197 156.28984006436534 chr16 90354753 258134265 2.8568974672533276 191.43352870148598 chr17 81195210 260463979 3.2078737033871825 259.92212872746757 chr18 78077248 222597007 2.850984284179688 249.5030489203165 chr19 59128983 74493319 1.2598444150476933 52.60681967253802 chr20 63025520 383804142 6.089662441499888 443.2493961160068 chr21 48129895 79376150 1.6492067975631362 83.33088054117404 chr22 51304566 101519149 1.9787546589907807 93.63471435730078 chrMT 16571 871010 52.562307645887394 89.28635421835983 chrX 155270560 123975474 0.7984480380569247 53.865231636194274 chrY 59373566 11087745 0.18674547861922255 12.256031567759887