BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046454.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 = 5,776,796 number of mapped reads = 5,698,302 (98.64%) number of supplementary alignments = 59,448 (1.03%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,865,848 number of mapped paired reads (second in pair) = 2,832,454 number of mapped paired reads (both in pair) = 5,639,864 number of mapped paired reads (singletons) = 58,438 number of mapped bases = 508,241,177 bp number of sequenced bases = 508,106,596 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,866,633 duplication rate = 47.26% >>>>>>> Insert size mean insert size = 109,922.3318 std insert size = 3,272,335.1757 median insert size = 102 >>>>>>> Mapping quality mean mapping quality = 52.6583 >>>>>>> ACTG content number of A's = 148,135,358 bp (29.15%) number of C's = 106,788,921 bp (21.02%) number of T's = 142,150,389 bp (27.98%) number of G's = 110,992,408 bp (21.84%) number of N's = 39,520 bp (0.01%) GC percentage = 42.86% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 2,132,690 number of insertions = 37,877 mapped reads with insertion percentage = 0.65% number of deletions = 48,284 mapped reads with deletion percentage = 0.83% homopolymer indels = 46.56% >>>>>>> Coverage mean coverageData = 0.1642X std coverageData = 10.2042X There is a 1.87% of reference with a coverageData >= 1X There is a 1.16% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.06% 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 0.06% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.05% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 78671391 0.31563167499590705 16.303300099755965 chr2 243199373 43247340 0.17782669201207194 9.120420352745318 chr3 198022430 26822849 0.13545358977768326 7.263344331943299 chr4 191154276 15884301 0.08309676002225554 5.040614197638837 chr5 180915260 31619661 0.17477608577629106 9.499162415864436 chr6 171115067 24058683 0.14059944236237246 5.991880456489722 chr7 159138663 32532243 0.20442702223783293 9.76867634475213 chr8 146364022 52861259 0.36116292978065334 18.50410913051265 chr9 141213431 10498952 0.07434811211406654 5.062528683283662 chr10 135534747 16184841 0.11941469887423038 6.732628737666963 chr11 135006516 17977902 0.13316321709983242 8.224252428766631 chr12 133851895 14281297 0.10669476887122144 7.2845967878035776 chr13 115169878 12599279 0.10939734606647755 6.235726587742703 chr14 107349540 24453968 0.22779760397669147 12.733914017873547 chr15 102531392 9314438 0.09084474343233338 4.433608488718305 chr16 90354753 37963204 0.42015724396922427 25.708224858941904 chr17 81195210 22357616 0.2753563418334653 11.013873725848098 chr18 78077248 6104230 0.0781819307975609 4.353084117143087 chr19 59128983 5016067 0.08483262768108155 3.9505032390160735 chr20 63025520 8783015 0.13935648607103915 9.087355057512042 chr21 48129895 2338707 0.04859156663441713 4.494519041319351 chr22 51304566 2861669 0.0557780568692463 2.569210771084928 chrMT 16571 33669 2.031802546617585 2.0010151256252056 chrX 155270560 11670370 0.07516151162203576 5.307658957818231 chrY 59373566 104226 0.0017554276595075997 0.10009207168598588