BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708628.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,309,753 number of mapped reads = 2,436,875 (73.63%) number of supplementary alignments = 783 (0.02%) number of secondary alignments = 0 number of mapped bases = 118,827,848 bp number of sequenced bases = 118,805,776 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,017 duplication rate = 2.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9078 >>>>>>> ACTG content number of A's = 35,193,053 bp (29.62%) number of C's = 22,358,871 bp (18.82%) number of T's = 37,413,898 bp (31.49%) number of G's = 23,829,684 bp (20.06%) number of N's = 10,270 bp (0.01%) GC percentage = 38.88% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 746,517 number of insertions = 5,524 mapped reads with insertion percentage = 0.23% number of deletions = 14,251 mapped reads with deletion percentage = 0.58% homopolymer indels = 48.41% >>>>>>> Coverage mean coverageData = 0.0384X std coverageData = 0.3906X There is a 3.3% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.06% 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 9290379 0.03727324314269211 0.7247086250620439 chr2 243199373 10299968 0.04235195129388759 0.38234532829164664 chr3 198022430 8222337 0.04152225078744867 0.23125603466109548 chr4 191154276 8112715 0.04244066713945756 0.23547462441476455 chr5 180915260 7575891 0.04187535645141267 0.23847905238360448 chr6 171115067 7202816 0.04209340607043096 0.298906131648512 chr7 159138663 6778350 0.042593986101290796 0.5638682203756605 chr8 146364022 6265328 0.042806476034117184 0.6786964882596402 chr9 141213431 4937887 0.0349675449780694 0.31831195195665674 chr10 135534747 5428306 0.04005102839052778 0.30053540017204594 chr11 135006516 5359474 0.03969789132251957 0.3372811656134115 chr12 133851895 5354141 0.040000487105543034 0.23637330337874715 chr13 115169878 4045379 0.03512532157062804 0.21293114578661018 chr14 107349540 3653222 0.03403109133024697 0.22573008222730584 chr15 102531392 3319807 0.03237844464259297 0.20277138384646676 chr16 90354753 2989228 0.03308324023640461 0.22401320419605159 chr17 81195210 2800729 0.03449377124586536 0.2633458969459366 chr18 78077248 3307921 0.04236728476905333 0.6381879515172294 chr19 59128983 1961820 0.03317865284440965 0.5111401323066114 chr20 63025520 2275820 0.03610949977088646 0.22837533836822135 chr21 48129895 1580816 0.0328447838915917 0.222436482120617 chr22 51304566 1143558 0.022289595043061078 0.16676872344881868 chrMT 16571 22471 1.3560436907851066 1.4254565994487667 chrX 155270560 6641145 0.04277143716104328 0.27254895769639154 chrY 59373566 258340 0.004351094559487971 0.08693761158928938