BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083638.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 = 2,867,413 number of mapped reads = 2,102,148 (73.31%) number of supplementary alignments = 14,876 (0.52%) number of secondary alignments = 0 number of mapped bases = 125,414,681 bp number of sequenced bases = 125,376,107 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,675 duplication rate = 3.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7488 >>>>>>> ACTG content number of A's = 35,671,729 bp (28.45%) number of C's = 25,046,034 bp (19.98%) number of T's = 36,371,987 bp (29.01%) number of G's = 28,269,090 bp (22.55%) number of N's = 17,267 bp (0.01%) GC percentage = 42.52% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,027,179 number of insertions = 8,530 mapped reads with insertion percentage = 0.4% number of deletions = 24,385 mapped reads with deletion percentage = 1.15% homopolymer indels = 45.21% >>>>>>> Coverage mean coverageData = 0.0405X std coverageData = 0.2797X There is a 3.56% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 10481877 0.042053564231641374 0.4335026817114301 chr2 243199373 10775763 0.04430835025220234 0.2964117203141451 chr3 198022430 8003745 0.04041837583752507 0.22187289420183828 chr4 191154276 7510093 0.039288124530366245 0.23212607902081794 chr5 180915260 7737383 0.042767995358711036 0.2298248219751831 chr6 171115067 7916451 0.046263903809242 0.27262138242975154 chr7 159138663 6578636 0.04133901765908389 0.3262561669129487 chr8 146364022 6966860 0.04759953918183527 0.3232974496605982 chr9 141213431 5593217 0.039608250861067174 0.269119388618215 chr10 135534747 5801566 0.04280500851932826 0.29031148650612876 chr11 135006516 5681165 0.04208067260990573 0.2488553724448232 chr12 133851895 6053973 0.045228892725052566 0.237759158215355 chr13 115169878 4152411 0.03605466179273022 0.20976981627957114 chr14 107349540 3902400 0.036352275007419686 0.2193811173212406 chr15 102531392 3751343 0.036587262952598947 0.21180220791709642 chr16 90354753 3833320 0.0424252169667267 0.24225433185791437 chr17 81195210 3571000 0.0439804269241991 0.2545947261778717 chr18 78077248 2891383 0.03703233751271561 0.40134982020580556 chr19 59128983 2246104 0.03798651500567835 0.3412001601280572 chr20 63025520 2350685 0.03729735192982144 0.2229456725366296 chr21 48129895 1713096 0.03559317966515406 0.22240159902269493 chr22 51304566 1425111 0.027777469163270965 0.18390693146788373 chrMT 16571 14877 0.8977732182728864 1.072655359059251 chrX 155270560 6158565 0.03966344296046849 0.23581980403083297 chrY 59373566 303657 0.005114346677442282 0.12385986164652772