BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006061.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 10,301,650 number of mapped reads = 9,007,560 (87.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,568,514 number of mapped paired reads (second in pair) = 4,439,046 number of mapped paired reads (both in pair) = 8,191,578 number of mapped paired reads (singletons) = 815,982 number of mapped bases = 347,675,906 bp number of sequenced bases = 347,636,535 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 558,518 duplication rate = 5.53% >>>>>>> Insert size mean insert size = 64,786.8878 std insert size = 2,477,697.8227 median insert size = 103 >>>>>>> Mapping quality mean mapping quality = 47.0999 >>>>>>> ACTG content number of A's = 94,315,867 bp (27.13%) number of C's = 75,633,033 bp (21.76%) number of T's = 97,640,986 bp (28.09%) number of G's = 80,032,569 bp (23.02%) number of N's = 14,080 bp (0%) GC percentage = 44.78% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 1,675,814 number of insertions = 11,652 mapped reads with insertion percentage = 0.13% number of deletions = 31,101 mapped reads with deletion percentage = 0.35% homopolymer indels = 46.4% >>>>>>> Coverage mean coverageData = 0.1123X std coverageData = 0.6248X There is a 6.51% of reference with a coverageData >= 1X There is a 2.68% of reference with a coverageData >= 2X There is a 1.1% of reference with a coverageData >= 3X There is a 0.47% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 29664317 0.11901401441242547 0.6985263397859001 chr2 243199373 30701441 0.1262398032580454 0.6895671988537599 chr3 198022430 24161378 0.1220133395999635 0.5381991283278375 chr4 191154276 21514358 0.11254970827856343 0.534473765438159 chr5 180915260 21139335 0.11684661094923668 0.5261627869529303 chr6 171115067 20507699 0.11984741822881091 0.5967426206530263 chr7 159138663 18981341 0.1192754836704893 0.8906323237312657 chr8 146364022 17395944 0.11885396262204383 0.6486135773704353 chr9 141213431 14840361 0.10509171043369098 0.573468301707833 chr10 135534747 16716601 0.12333812081414075 0.5636873413438274 chr11 135006516 16064279 0.11898891606091072 0.9889351074788686 chr12 133851895 15918263 0.1189244500423397 0.5341724052656824 chr13 115169878 10769572 0.09351031873108348 0.47217880462137746 chr14 107349540 10869046 0.10124911573910797 0.510225966050325 chr15 102531392 10946062 0.10675815266411286 0.5116908770494406 chr16 90354753 10802275 0.11955403165121817 0.5763189346151114 chr17 81195210 10253263 0.12627916104903233 0.6366547593253085 chr18 78077248 9345611 0.11969698266004458 0.7641333900904428 chr19 59128983 7467205 0.126286714588005 0.7140017543450609 chr20 63025520 8146914 0.1292637331671361 0.5647458227288336 chr21 48129895 4484280 0.09317036739847448 0.5197080792591641 chr22 51304566 4684513 0.0913079159465066 0.5030303592977088 chrMT 16571 21876 1.3201375897652525 2.027141154546428 chrX 155270560 10265242 0.06611196610613113 0.43000311379159906 chrY 59373566 2014730 0.033933114275130453 0.30832562800816304