BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094138.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 603,596 number of mapped reads = 587,891 (97.4%) number of supplementary alignments = 28,804 (4.77%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 294,869 number of mapped paired reads (second in pair) = 293,022 number of mapped paired reads (both in pair) = 585,476 number of mapped paired reads (singletons) = 2,415 number of mapped bases = 85,167,007 bp number of sequenced bases = 85,014,470 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 608,087 duplication rate = 41.26% >>>>>>> Insert size mean insert size = 18,736.798 std insert size = 1,461,331.7442 median insert size = 231 >>>>>>> Mapping quality mean mapping quality = 14.5445 >>>>>>> ACTG content number of A's = 25,478,255 bp (29.97%) number of C's = 17,676,375 bp (20.79%) number of T's = 23,842,465 bp (28.05%) number of G's = 18,016,391 bp (21.19%) number of N's = 984 bp (0%) GC percentage = 41.98% >>>>>>> Mismatches and indels general error rate = 0.0165 number of mismatches = 1,345,710 number of insertions = 31,675 mapped reads with insertion percentage = 5.33% number of deletions = 60,149 mapped reads with deletion percentage = 10.04% homopolymer indels = 55.94% >>>>>>> Coverage mean coverageData = 0.0275X std coverageData = 43.3572X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% 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 600528 0.0024093340172660995 2.6657491025381312 chr2 243199373 430425 0.0017698442010374755 1.0300048109244877 chr3 198022430 803792 0.004059095729711023 4.170048355577899 chr4 191154276 54040 2.8270358963876905E-4 0.15278358870938538 chr5 180915260 99721 5.51202811747334E-4 0.24369059821620426 chr6 171115067 144839 8.464421195592321E-4 0.5070706239805801 chr7 159138663 1132370 0.00711561840883381 3.425751242107875 chr8 146364022 48787 3.333264509498106E-4 0.1546722617549538 chr9 141213431 36843 2.6090294484807183E-4 0.0898223405520092 chr10 135534747 143137 0.001056090804522622 0.4071126941893983 chr11 135006516 70123 5.194045597028813E-4 0.1879461437269255 chr12 133851895 755323 0.005642975768105487 6.5054994328106694 chr13 115169878 23952 2.079710460403544E-4 0.06751300875047979 chr14 107349540 20102 1.8725743957542809E-4 0.04989597195578358 chr15 102531392 201839 0.001968558078290793 2.1917664233048413 chr16 90354753 23881 2.643026427176443E-4 0.10300908573762296 chr17 81195210 21998 2.709273120914399E-4 0.080552519849483 chr18 78077248 60439 7.740923450580635E-4 0.6306285662825328 chr19 59128983 24049 4.067210153098693E-4 0.13205981299277808 chr20 63025520 34142 5.417170695299301E-4 0.12204705249781633 chr21 48129895 3384 7.030973161275336E-5 0.021777357764626006 chr22 51304566 20297 3.956178091439269E-4 0.19332760383256042 chrMT 16571 72819629 4394.401605213928 17931.346917519004 chrX 155270560 7560754 0.04869406022622705 31.915059498312978 chrY 59373566 32613 5.492848450436681E-4 0.17088589219164427