BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089568.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 = 21,024,312 number of mapped reads = 16,644,375 (79.17%) number of supplementary alignments = 664 (0%) number of secondary alignments = 0 number of mapped bases = 769,249,671 bp number of sequenced bases = 769,086,045 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,725,045 duplication rate = 7.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6032 >>>>>>> ACTG content number of A's = 246,741,858 bp (32.08%) number of C's = 155,759,082 bp (20.25%) number of T's = 203,371,197 bp (26.44%) number of G's = 163,171,465 bp (21.22%) number of N's = 42,443 bp (0.01%) GC percentage = 41.47% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 3,541,690 number of insertions = 36,256 mapped reads with insertion percentage = 0.22% number of deletions = 109,608 mapped reads with deletion percentage = 0.66% homopolymer indels = 43.09% >>>>>>> Coverage mean coverageData = 0.2485X std coverageData = 1.3158X There is a 13.61% of reference with a coverageData >= 1X There is a 5.21% of reference with a coverageData >= 2X There is a 2.43% of reference with a coverageData >= 3X There is a 1.27% of reference with a coverageData >= 4X There is a 0.72% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.27% of reference with a coverageData >= 7X There is a 0.18% of reference with a coverageData >= 8X There is a 0.12% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 60773532 0.24382499733069873 1.7903507606065667 chr2 243199373 65023584 0.2673673998328935 1.547649415327945 chr3 198022430 50432826 0.2546823912826441 0.8604095125201434 chr4 191154276 51768191 0.27081890127323127 0.9602010889489014 chr5 180915260 47917476 0.26486143844361165 0.8915192979609149 chr6 171115067 43998252 0.25712669708974256 0.9968719844661077 chr7 159138663 42395797 0.2664078998828839 1.7438880257026073 chr8 146364022 39765728 0.27169059347111957 2.468921933093605 chr9 141213431 32330488 0.22894768416185568 1.1891754851396128 chr10 135534747 35969043 0.2653861374751377 1.2758692616322977 chr11 135006516 34908839 0.2585715122076034 1.2456365219666694 chr12 133851895 35297050 0.26370228079326036 0.9318907249791293 chr13 115169878 25375651 0.22033235982068158 0.8171190110966832 chr14 107349540 24060574 0.2241329958190785 0.9778685864774253 chr15 102531392 21677141 0.21141955236499665 0.7921853739212512 chr16 90354753 21241764 0.23509293418133742 0.9408510959199268 chr17 81195210 19746847 0.24320211746481105 0.9913630246611991 chr18 78077248 20810918 0.26654266810223637 1.891642278236128 chr19 59128983 13196564 0.22318266492085614 1.6736525978240242 chr20 63025520 15970094 0.25339091212575476 0.9315818658541276 chr21 48129895 10060230 0.2090224796875206 0.9512328670275433 chr22 51304566 8349821 0.16275005620357455 0.7126474625574746 chrMT 16571 162993 9.836038863074045 9.431739635194525 chrX 155270560 45863844 0.2953801673672073 1.1935836863462788 chrY 59373566 2152424 0.03625222712747286 0.5442437678961601