BamQC report ----------------------------------- >>>>>>> Input bam file = SRR090135.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 = 11,754,983 number of mapped reads = 10,148,856 (86.34%) number of supplementary alignments = 86,960 (0.74%) number of secondary alignments = 0 number of mapped bases = 610,382,910 bp number of sequenced bases = 610,174,021 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,415,979 duplication rate = 10.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1369 >>>>>>> ACTG content number of A's = 171,610,169 bp (28.12%) number of C's = 114,024,669 bp (18.69%) number of T's = 187,026,071 bp (30.65%) number of G's = 137,127,391 bp (22.47%) number of N's = 385,721 bp (0.06%) GC percentage = 41.16% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 4,000,487 number of insertions = 42,422 mapped reads with insertion percentage = 0.41% number of deletions = 126,012 mapped reads with deletion percentage = 1.23% homopolymer indels = 47.33% >>>>>>> Coverage mean coverageData = 0.1972X std coverageData = 1.5829X There is a 11.33% of reference with a coverageData >= 1X There is a 4.43% of reference with a coverageData >= 2X There is a 1.86% of reference with a coverageData >= 3X There is a 0.83% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% 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 49278464 0.1977064843501433 2.32894088328549 chr2 243199373 64505582 0.26523745190741094 2.37219047083165 chr3 198022430 57497000 0.2903559965403919 0.8704931616795434 chr4 191154276 32283184 0.16888549226071198 0.7292812193741403 chr5 180915260 27977529 0.15464438433772806 0.6298538750357933 chr6 171115067 34180227 0.19974995539112872 1.0215024652450204 chr7 159138663 44433571 0.27921292137536685 2.6234679993070595 chr8 146364022 55044948 0.37608250475653093 3.6444660984617583 chr9 141213431 19238957 0.1362402773146982 1.140391548620986 chr10 135534747 18566896 0.13698993365885723 1.12448043780242 chr11 135006516 25148570 0.18627671274770174 1.065231987253739 chr12 133851895 21958175 0.16404829382505193 0.762509951821004 chr13 115169878 18810616 0.16332930386537356 0.6241557185765695 chr14 107349540 21537178 0.2006266445110058 0.7962593967843808 chr15 102531392 15787270 0.15397498943543067 0.7496120395093294 chr16 90354753 11654939 0.1289908788749608 0.6509329971441813 chr17 81195210 11522804 0.14191482477845677 0.716561286468948 chr18 78077248 23256579 0.2978662746924687 1.9740854376412784 chr19 59128983 9783538 0.1654609550784934 1.5552322336018127 chr20 63025520 14118979 0.22402003188549655 0.805102355558885 chr21 48129895 8940398 0.1857556098969258 0.7224604618088614 chr22 51304566 4529607 0.0882885745490957 0.44082766180274546 chrMT 16571 121227 7.315611610645103 5.3609384638008635 chrX 155270560 18845505 0.12137204245286422 0.7351717994460478 chrY 59373566 1361167 0.022925471581073636 0.7616458063069781