BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089751.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 = 34,641,887 number of mapped reads = 29,250,938 (84.44%) number of supplementary alignments = 1,307 (0%) number of secondary alignments = 0 number of mapped bases = 1,385,842,257 bp number of sequenced bases = 1,385,591,534 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,596,918 duplication rate = 11.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0044 >>>>>>> ACTG content number of A's = 425,519,475 bp (30.71%) number of C's = 272,270,815 bp (19.65%) number of T's = 401,023,101 bp (28.94%) number of G's = 286,577,017 bp (20.68%) number of N's = 201,126 bp (0.01%) GC percentage = 40.33% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 5,860,177 number of insertions = 50,692 mapped reads with insertion percentage = 0.17% number of deletions = 166,937 mapped reads with deletion percentage = 0.57% homopolymer indels = 47.91% >>>>>>> Coverage mean coverageData = 0.4477X std coverageData = 2.6266X There is a 14.54% of reference with a coverageData >= 1X There is a 8.8% of reference with a coverageData >= 2X There is a 5.88% of reference with a coverageData >= 3X There is a 4.06% of reference with a coverageData >= 4X There is a 2.87% of reference with a coverageData >= 5X There is a 2.05% of reference with a coverageData >= 6X There is a 1.49% of reference with a coverageData >= 7X There is a 1.09% of reference with a coverageData >= 8X There is a 0.81% of reference with a coverageData >= 9X There is a 0.6% of reference with a coverageData >= 10X There is a 0.46% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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% 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 108225406 0.43420315490407546 4.754382044293039 chr2 243199373 116990897 0.4810493364224257 2.2167453343375536 chr3 198022430 99575721 0.5028507174667032 1.6903684513733543 chr4 191154276 95526750 0.4997364013975811 1.7574755854051147 chr5 180915260 90189462 0.4985177148682759 1.7081675137730583 chr6 171115067 86468626 0.505324443463532 1.9075001656139559 chr7 159138663 72436609 0.45517919803058793 2.5675776972133977 chr8 146364022 72239526 0.49356067845689566 5.703916765798461 chr9 141213431 57628388 0.40809424140399225 2.0792321564885317 chr10 135534747 63200293 0.46630324989650074 2.17132415607949 chr11 135006516 64112916 0.474887567648957 2.2169334311935596 chr12 133851895 62619433 0.4678262717162129 1.733800212132472 chr13 115169878 48216066 0.41865170682910685 1.5560304265023146 chr14 107349540 42567867 0.3965351598153099 1.5849105186932662 chr15 102531392 37026002 0.36111869036167965 1.4224663518342249 chr16 90354753 35077085 0.388215161188034 1.5502502785425616 chr17 81195210 32852127 0.40460671263735876 1.7785247287522443 chr18 78077248 37024937 0.47420904230640915 3.9265251123633598 chr19 59128983 21938671 0.37103075153516507 3.225933514334821 chr20 63025520 26971262 0.4279419194002683 1.6345660767596621 chr21 48129895 16680950 0.3465818905277063 1.634062329766542 chr22 51304566 13750069 0.2680086797732584 1.2077465060442552 chrMT 16571 178268 10.757829943877859 9.565920853760968 chrX 155270560 80557929 0.5188229436410869 1.9298391294281971 chrY 59373566 3786997 0.06378254255437513 1.1232281524782373