BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472545.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,407,146 number of mapped reads = 18,183,899 (98.79%) number of supplementary alignments = 63,200 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,133,411 number of mapped paired reads (second in pair) = 9,050,488 number of mapped paired reads (both in pair) = 18,055,052 number of mapped paired reads (singletons) = 128,847 number of mapped bases = 1,792,237,822 bp number of sequenced bases = 1,792,021,364 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,185,509 duplication rate = 47.26% >>>>>>> Insert size mean insert size = 28,865.202 std insert size = 1,687,170.3044 median insert size = 241 >>>>>>> Mapping quality mean mapping quality = 55.0079 >>>>>>> ACTG content number of A's = 494,731,685 bp (27.61%) number of C's = 403,777,851 bp (22.53%) number of T's = 492,228,339 bp (27.47%) number of G's = 401,006,459 bp (22.38%) number of N's = 277,030 bp (0.02%) GC percentage = 44.91% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 11,184,554 number of insertions = 93,498 mapped reads with insertion percentage = 0.51% number of deletions = 86,193 mapped reads with deletion percentage = 0.47% homopolymer indels = 45.44% >>>>>>> Coverage mean coverageData = 0.5789X std coverageData = 16.7133X There is a 5.7% of reference with a coverageData >= 1X There is a 2.44% of reference with a coverageData >= 2X There is a 1.03% of reference with a coverageData >= 3X There is a 0.72% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.35% 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 0.31% 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 0.29% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.25% 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 0.24% 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 0.23% 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 0.22% 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 0.19% 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 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 201778286 0.8095397523603362 21.186379910534068 chr2 243199373 132714951 0.5457043304137137 16.287753903852078 chr3 198022430 176936300 0.8935164566963449 20.421709718465312 chr4 191154276 90146799 0.4715918518087453 17.784589365516307 chr5 180915260 103668656 0.5730232817286944 18.126090971564746 chr6 171115067 98103788 0.5733205714725285 14.379110580654299 chr7 159138663 60728478 0.38160731562762973 9.971902585269817 chr8 146364022 79237970 0.541376008374517 14.496652664535736 chr9 141213431 112560474 0.7970946757890189 17.319300347163118 chr10 135534747 53707098 0.3962607315746124 14.963396456234996 chr11 135006516 80078173 0.593143022815284 17.3531683881111 chr12 133851895 128274890 0.9583345084505528 24.988438305129183 chr13 115169878 45798712 0.3976622429000055 13.346370234832023 chr14 107349540 62586392 0.5830149994122006 16.947192368735635 chr15 102531392 44068215 0.4298021721971745 12.273282147857728 chr16 90354753 45412419 0.5026013296721645 12.47176259016201 chr17 81195210 66482506 0.8187983749287674 17.364273792865077 chr18 78077248 31739114 0.4065091279856585 16.29591842574827 chr19 59128983 26527708 0.4486413710176615 12.014497906014324 chr20 63025520 46010197 0.7300248692910427 26.417601030732904 chr21 48129895 7102563 0.1475707146254942 4.965287749916753 chr22 51304566 17097253 0.3332501243651491 8.257979016568195 chrMT 16571 2065 0.12461529177478728 0.48969030807296365 chrX 155270560 78757149 0.5072252524883017 12.293709196857105 chrY 59373566 2717666 0.04577232231596128 1.2879710741019232