BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081221.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 = 2,271,479 number of mapped reads = 1,980,747 (87.2%) number of supplementary alignments = 26,413 (1.16%) number of secondary alignments = 0 number of mapped bases = 129,035,744 bp number of sequenced bases = 128,987,377 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,183 duplication rate = 4.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1588 >>>>>>> ACTG content number of A's = 36,774,203 bp (28.51%) number of C's = 25,068,609 bp (19.43%) number of T's = 39,356,142 bp (30.51%) number of G's = 27,780,457 bp (21.54%) number of N's = 7,966 bp (0.01%) GC percentage = 40.97% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,163,346 number of insertions = 9,683 mapped reads with insertion percentage = 0.48% number of deletions = 29,578 mapped reads with deletion percentage = 1.48% homopolymer indels = 47.84% >>>>>>> Coverage mean coverageData = 0.0417X std coverageData = 0.3046X There is a 3.33% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% 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% 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 13225960 0.05306289688241138 0.4547004428933222 chr2 243199373 8488501 0.034903465807866206 0.34624138764141327 chr3 198022430 7302246 0.03687585290211821 0.23361641043150924 chr4 191154276 4890475 0.025583916312706498 0.20289642705743527 chr5 180915260 9136866 0.05050356725021427 0.2717846153183393 chr6 171115067 8703845 0.050865450673610174 0.2983232337322554 chr7 159138663 6106371 0.038371385588428626 0.3108212851132712 chr8 146364022 8450093 0.05773340254342013 0.3820306903739526 chr9 141213431 3757485 0.02660855255333326 0.24643995413522954 chr10 135534747 4134947 0.030508390590052895 0.31111065779699026 chr11 135006516 7033275 0.05209581884181057 0.34157410109242103 chr12 133851895 3533259 0.026396779813987692 0.19756466811760479 chr13 115169878 3913864 0.03398339972193076 0.2251827032531206 chr14 107349540 4849555 0.04517536824098175 0.2641204385519787 chr15 102531392 4655103 0.045401734134263974 0.26346585775552384 chr16 90354753 4125417 0.045657996541698255 0.2681354858950259 chr17 81195210 2238704 0.027571872774268334 0.21462612845485493 chr18 78077248 3240899 0.041508878489159864 0.37746485800095725 chr19 59128983 3545416 0.05996071334424947 0.3797242548458724 chr20 63025520 3227898 0.05121572975518488 0.27595562573864757 chr21 48129895 2083736 0.043294006770636 0.26087262022016106 chr22 51304566 1033420 0.02014284654508139 0.16877258304360893 chrMT 16571 85743 5.174280369319896 4.296946689253166 chrX 155270560 10897375 0.07018313709952485 0.3377636044768194 chrY 59373566 375291 0.006320843184658978 0.128261029669094