BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714167.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 841,976 number of mapped reads = 765,122 (90.87%) number of supplementary alignments = 10,820 (1.29%) number of secondary alignments = 0 number of mapped bases = 107,706,164 bp number of sequenced bases = 105,077,519 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 752,687 duplication rate = 36.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 24.4099 >>>>>>> ACTG content number of A's = 23,970,245 bp (22.81%) number of C's = 27,107,998 bp (25.8%) number of T's = 22,759,105 bp (21.66%) number of G's = 31,239,383 bp (29.73%) number of N's = 788 bp (0%) GC percentage = 55.53% >>>>>>> Mismatches and indels general error rate = 0.0397 number of mismatches = 4,130,852 number of insertions = 39,367 mapped reads with insertion percentage = 5% number of deletions = 554,114 mapped reads with deletion percentage = 71.09% homopolymer indels = 7.62% >>>>>>> Coverage mean coverageData = 0.0348X std coverageData = 103.5395X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% 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 1738808 0.006976143100562225 3.0998127336774863 chr2 243199373 4068594 0.01672945924905818 8.041378046303306 chr3 198022430 2772975 0.014003337904700998 4.254820321681852 chr4 191154276 261643 0.0013687530589166627 0.5628501128266165 chr5 180915260 2036614 0.011257281447678874 7.201570750104267 chr6 171115067 1685328 0.00984909178102943 3.7426677434019915 chr7 159138663 227476 0.0014294200775081289 0.5597681876449343 chr8 146364022 425871 0.0029096699734037098 1.1506446962498316 chr9 141213431 368301 0.002608115937640521 1.1245490373959697 chr10 135534747 938053 0.0069211255472369755 3.1224089573910985 chr11 135006516 4679923 0.03466442316013844 27.081119732514008 chr12 133851895 1174180 0.008772232922066588 4.514876190402009 chr13 115169878 935508 0.008122853095320636 4.176607722024936 chr14 107349540 1976520 0.018412002510676803 5.5688876324030065 chr15 102531392 114013 0.0011119813920013881 0.5148170649676374 chr16 90354753 198222 0.0021938192891745273 0.7717901157998389 chr17 81195210 790479 0.009735537354974512 5.129923984196937 chr18 78077248 550887 0.007055666203808823 4.111222845027817 chr19 59128983 1169388 0.019776900272409557 8.944862149871062 chr20 63025520 78780046 1.2499705833446515 723.945003573468 chr21 48129895 323667 0.006724864037205982 2.3421935546514163 chr22 51304566 88955 0.001733861270749274 0.8146865167541835 chrMT 16571 329075 19.858487719509988 168.09361994969768 chrX 155270560 1834232 0.011813134440939737 5.173468018831519 chrY 59373566 237406 0.003998513412517618 1.260904940498339