BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089403.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 = 23,524,958 number of mapped reads = 21,685,914 (92.18%) number of supplementary alignments = 152,608 (0.65%) number of secondary alignments = 0 number of mapped bases = 1,424,882,341 bp number of sequenced bases = 1,424,405,984 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,781,336 duplication rate = 14.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2549 >>>>>>> ACTG content number of A's = 379,362,715 bp (26.63%) number of C's = 271,034,791 bp (19.03%) number of T's = 439,947,449 bp (30.89%) number of G's = 333,963,981 bp (23.45%) number of N's = 97,048 bp (0.01%) GC percentage = 42.47% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 9,062,244 number of insertions = 89,533 mapped reads with insertion percentage = 0.41% number of deletions = 275,475 mapped reads with deletion percentage = 1.26% homopolymer indels = 46.09% >>>>>>> Coverage mean coverageData = 0.4603X std coverageData = 3.0069X There is a 15.44% of reference with a coverageData >= 1X There is a 9.1% of reference with a coverageData >= 2X There is a 5.83% of reference with a coverageData >= 3X There is a 3.9% of reference with a coverageData >= 4X There is a 2.69% of reference with a coverageData >= 5X There is a 1.91% of reference with a coverageData >= 6X There is a 1.39% of reference with a coverageData >= 7X There is a 1.03% of reference with a coverageData >= 8X There is a 0.77% of reference with a coverageData >= 9X There is a 0.59% of reference with a coverageData >= 10X There is a 0.46% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 120925488 0.4851562155185162 4.871992074085754 chr2 243199373 159690121 0.6566222561766226 3.9450624012666697 chr3 198022430 97243223 0.4910717588911519 1.695970239800928 chr4 191154276 67811227 0.35474606385472646 1.8963361816821243 chr5 180915260 69651845 0.3849970698989129 1.5427398276814808 chr6 171115067 83850892 0.4900263516829877 2.304917862693419 chr7 159138663 76875775 0.48307415401623677 4.451058043720845 chr8 146364022 80113476 0.5473577106264543 3.2383905925821543 chr9 141213431 75292718 0.533183830084831 3.2121639943856657 chr10 135534747 51594703 0.3806750972870448 3.49655517968637 chr11 135006516 62924442 0.4660844814334739 3.2355420368933436 chr12 133851895 73701186 0.5506174268208903 1.9254356295723793 chr13 115169878 35082209 0.3046127130567942 1.3109803583108341 chr14 107349540 26061539 0.242772712393551 1.8487147124665697 chr15 102531392 36260354 0.35365124078292043 1.4456749927907173 chr16 90354753 34876324 0.38599324155089 1.9483367760085195 chr17 81195210 33741692 0.4155625929165033 2.0924744050002526 chr18 78077248 45618643 0.5842757546987312 4.792875936804295 chr19 59128983 30450529 0.5149848256311123 4.38127555846516 chr20 63025520 30493314 0.48382486967184085 1.8240907725293238 chr21 48129895 14350878 0.2981697342161249 1.8683095602728472 chr22 51304566 20908801 0.40754269317861497 1.5576237847558154 chrMT 16571 110199 6.650111640818297 6.259677204594729 chrX 155270560 93653093 0.6031606571136215 2.421348569101823 chrY 59373566 3599670 0.06062748530212923 1.4132393794680707