BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046535.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 12,261,316 number of mapped reads = 11,700,259 (95.42%) number of supplementary alignments = 47,917 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,878,840 number of mapped paired reads (second in pair) = 5,821,419 number of mapped paired reads (both in pair) = 11,628,118 number of mapped paired reads (singletons) = 72,141 number of mapped bases = 1,149,654,796 bp number of sequenced bases = 1,149,351,170 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,854,847 duplication rate = 32.02% >>>>>>> Insert size mean insert size = 18,353.6781 std insert size = 1,335,774.3637 median insert size = 158 >>>>>>> Mapping quality mean mapping quality = 53.7878 >>>>>>> ACTG content number of A's = 332,549,141 bp (28.93%) number of C's = 241,489,614 bp (21.01%) number of T's = 333,282,108 bp (29%) number of G's = 241,916,977 bp (21.05%) number of N's = 113,330 bp (0.01%) GC percentage = 42.06% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 4,222,364 number of insertions = 94,279 mapped reads with insertion percentage = 0.79% number of deletions = 113,390 mapped reads with deletion percentage = 0.95% homopolymer indels = 48.89% >>>>>>> Coverage mean coverageData = 0.3714X std coverageData = 24.2863X There is a 5.35% of reference with a coverageData >= 1X There is a 2.33% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.07% of reference with a coverageData >= 28X There is a 0.07% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.06% of reference with a coverageData >= 31X There is a 0.06% of reference with a coverageData >= 32X There is a 0.06% of reference with a coverageData >= 33X There is a 0.06% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.06% of reference with a coverageData >= 41X There is a 0.06% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 157221137 0.6307753070753633 30.79666295331515 chr2 243199373 96946181 0.39862841669414995 22.767256578755656 chr3 198022430 72050070 0.3638480246909403 23.953155475497397 chr4 191154276 27410082 0.1433924606530905 7.005502769116184 chr5 180915260 98677263 0.5454336079775691 38.03390398550145 chr6 171115067 38678411 0.22603743596699175 11.491945790638972 chr7 159138663 118918951 0.7472662441558906 35.22342573493003 chr8 146364022 89422290 0.6109581355997445 31.77941388580834 chr9 141213431 34549917 0.2446645248637858 14.3778007475767 chr10 135534747 45148427 0.33311330119648214 21.910348338316922 chr11 135006516 12621411 0.09348742100714605 5.244351665342483 chr12 133851895 57357246 0.4285127677871128 28.92593291973354 chr13 115169878 31383408 0.2724966679221454 19.605185557787276 chr14 107349540 47176234 0.43946377413447696 24.03636019528042 chr15 102531392 20274489 0.19773933235979085 9.531039781989614 chr16 90354753 76007827 0.8412155916136476 49.70780122636619 chr17 81195210 34095527 0.41992042387722134 17.010678976528713 chr18 78077248 13147380 0.16838938790465566 5.6082847925633 chr19 59128983 10028133 0.16959758973023434 6.472098079808037 chr20 63025520 17633952 0.27979066257604857 11.621460218186174 chr21 48129895 7916368 0.1644792285543112 14.673489832751141 chr22 51304566 5460610 0.10643516602401432 4.858583044734992 chrMT 16571 69918 4.219298774968318 2.8805716189806554 chrX 155270560 37300573 0.2402295258032173 27.027322616674844 chrY 59373566 158991 0.0026778078311819773 0.17022550349052476