BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818890.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,717,020 number of mapped reads = 1,694,552 (98.69%) number of supplementary alignments = 24,338 (1.42%) number of secondary alignments = 0 number of mapped bases = 157,015,013 bp number of sequenced bases = 156,915,478 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 290,710 duplication rate = 14.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3355 >>>>>>> ACTG content number of A's = 43,416,388 bp (27.67%) number of C's = 33,220,638 bp (21.17%) number of T's = 44,872,725 bp (28.6%) number of G's = 35,403,508 bp (22.56%) number of N's = 2,219 bp (0%) GC percentage = 43.73% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 941,752 number of insertions = 23,021 mapped reads with insertion percentage = 1.31% number of deletions = 50,054 mapped reads with deletion percentage = 2.88% homopolymer indels = 40.94% >>>>>>> Coverage mean coverageData = 0.0507X std coverageData = 0.6363X There is a 3.76% of reference with a coverageData >= 1X There is a 0.82% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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% 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 15507105 0.06221491018872928 0.9814050514092728 chr2 243199373 11954032 0.04915321882840545 0.9270092838589096 chr3 198022430 9615607 0.04855817091023477 0.27871029870688036 chr4 191154276 7436547 0.0389033777094267 0.35011322780712073 chr5 180915260 6882955 0.03804518756460898 0.26514245824191474 chr6 171115067 7460593 0.04359986020401114 0.3015041965308319 chr7 159138663 13645657 0.08574696269755641 1.3530588695267265 chr8 146364022 13033848 0.08905090077396206 0.5149608795342813 chr9 141213431 5704711 0.04039779332321442 0.505306375435742 chr10 135534747 7486794 0.05523892703322787 0.904055209668137 chr11 135006516 7089293 0.05251074696276141 0.36123355915467514 chr12 133851895 6258721 0.046758553549055094 0.2771928185088882 chr13 115169878 4519134 0.03923885375653519 0.24696613347062663 chr14 107349540 4617526 0.04301393373460194 0.28584361385675766 chr15 102531392 4454287 0.043443153488055636 0.26265560083103545 chr16 90354753 4162043 0.0460633542985835 0.6835970208627992 chr17 81195210 4477946 0.055150371555169324 0.3894214161060055 chr18 78077248 2903348 0.03718558318039079 0.6115217921911139 chr19 59128983 3018691 0.05105264536682459 0.8847641823018358 chr20 63025520 6834972 0.10844768912656333 0.4657273102808021 chr21 48129895 1513786 0.03145209437917951 0.27838839888837724 chr22 51304566 1651728 0.03219456139634823 0.26851703357512274 chrMT 16571 269560 16.26697242170056 10.893470060042096 chrX 155270560 5934952 0.03822329229700724 0.3123900384732366 chrY 59373566 581177 0.00978848061778873 0.7765013140082411