BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080958.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 5,372,743 number of mapped reads = 4,687,968 (87.25%) number of supplementary alignments = 48,982 (0.91%) number of secondary alignments = 0 number of mapped bases = 313,652,340 bp number of sequenced bases = 313,535,078 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 363,340 duplication rate = 5.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7212 >>>>>>> ACTG content number of A's = 87,680,846 bp (27.97%) number of C's = 54,945,905 bp (17.52%) number of T's = 102,420,409 bp (32.67%) number of G's = 67,873,136 bp (21.65%) number of N's = 614,782 bp (0.2%) GC percentage = 39.17% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 3,210,956 number of insertions = 25,909 mapped reads with insertion percentage = 0.55% number of deletions = 71,117 mapped reads with deletion percentage = 1.5% homopolymer indels = 49.04% >>>>>>> Coverage mean coverageData = 0.1013X std coverageData = 0.8761X There is a 7.07% of reference with a coverageData >= 1X There is a 1.96% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 25470073 0.10218659796237779 1.5855933072138537 chr2 243199373 20830232 0.08565084581858688 0.723298131125913 chr3 198022430 27268485 0.13770402171107587 0.5002867391551544 chr4 191154276 19963466 0.10443640821301847 0.4819607686946305 chr5 180915260 22304391 0.1232863993894158 0.47644843585237023 chr6 171115067 26137924 0.1527505698840652 0.8942614862796409 chr7 159138663 15218773 0.09563215319962817 0.873284531169106 chr8 146364022 24236490 0.16559048917089747 1.8074377833341866 chr9 141213431 15931420 0.11281802224605675 0.9533037503207681 chr10 135534747 13421169 0.09902382449572138 0.6884333293269314 chr11 135006516 13608631 0.1007998088033025 0.6013644326372082 chr12 133851895 12690212 0.0948078620777091 0.44543907774970043 chr13 115169878 8354207 0.0725381249427042 0.35644449027265407 chr14 107349540 8713512 0.08116953272459296 0.5230334542948961 chr15 102531392 7450997 0.07267039737449385 0.3558833849215939 chr16 90354753 7195026 0.07963085240241873 0.5251204504312051 chr17 81195210 6579674 0.08103524826156618 0.4044442802723167 chr18 78077248 8204850 0.105086311443764 1.7730825321197254 chr19 59128983 5869750 0.09927026818641545 1.1150554043457481 chr20 63025520 4946729 0.07848771418308012 0.44160837359684013 chr21 48129895 7081174 0.1471263130742338 0.6446566924772651 chr22 51304566 2421893 0.04720618823673511 0.2818966662930089 chrMT 16571 87368 5.272343250256472 3.8397887311445817 chrX 155270560 8933239 0.057533372714054745 0.39510633809104595 chrY 59373566 732655 0.012339750656041107 0.2845275297450299