BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081923.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 = 2,751,694 number of mapped reads = 2,483,040 (90.24%) number of supplementary alignments = 33,483 (1.22%) number of secondary alignments = 0 number of mapped bases = 165,182,317 bp number of sequenced bases = 165,123,637 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,200 duplication rate = 2.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.721 >>>>>>> ACTG content number of A's = 45,449,536 bp (27.52%) number of C's = 32,361,649 bp (19.6%) number of T's = 48,629,947 bp (29.45%) number of G's = 38,680,801 bp (23.43%) number of N's = 1,704 bp (0%) GC percentage = 43.02% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,441,292 number of insertions = 14,758 mapped reads with insertion percentage = 0.59% number of deletions = 34,943 mapped reads with deletion percentage = 1.39% homopolymer indels = 43.05% >>>>>>> Coverage mean coverageData = 0.0534X std coverageData = 0.5984X There is a 4.73% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 13415938 0.05382509357920517 1.2149493202261432 chr2 243199373 13915585 0.05721883583967957 0.7765328063813295 chr3 198022430 10802654 0.05455267870412458 0.2593069503433069 chr4 191154276 10407217 0.05444407113341268 0.28827987417932555 chr5 180915260 9795535 0.05414432701807465 0.2581521723563638 chr6 171115067 9594570 0.056070866044776756 0.33785387718898086 chr7 159138663 9291047 0.058383342079479456 0.9112520091317678 chr8 146364022 8470132 0.05787031460504686 0.6219792369471902 chr9 141213431 7023606 0.049737521071915605 0.5703888890620841 chr10 135534747 7766482 0.05730251593711242 0.5581735809208872 chr11 135006516 7442651 0.05512808729913451 0.47372128395294405 chr12 133851895 7467961 0.05579271776466071 0.2691997004525665 chr13 115169878 4928253 0.04279116280734447 0.2259221783510896 chr14 107349540 4997533 0.04655383711937657 0.29996392169037345 chr15 102531392 4702787 0.045866801457255156 0.26181761217996397 chr16 90354753 4850655 0.053684558243438506 0.32511175916398577 chr17 81195210 4637322 0.05711324596611056 0.2995233112989159 chr18 78077248 4415842 0.05655734689829232 1.114519241910552 chr19 59128983 3828205 0.06474329179651205 0.890177631942449 chr20 63025520 3396481 0.05389056686878585 0.2687815848534322 chr21 48129895 2114119 0.043925277626306894 0.2696320924159979 chr22 51304566 1967661 0.0383525513109301 0.2124764625373064 chrMT 16571 27436 1.655663508539014 1.709092402383913 chrX 155270560 9427674 0.0607177175119353 0.3611041518677825 chrY 59373566 494971 0.008336555025177366 0.19215434500779602