BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818805.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 = 78,263 number of mapped reads = 73,795 (94.29%) number of supplementary alignments = 496 (0.63%) number of secondary alignments = 0 number of mapped bases = 4,996,672 bp number of sequenced bases = 4,994,624 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,596 duplication rate = 3.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7592 >>>>>>> ACTG content number of A's = 1,414,077 bp (28.31%) number of C's = 1,098,760 bp (22%) number of T's = 1,394,675 bp (27.92%) number of G's = 1,086,751 bp (21.76%) number of N's = 361 bp (0.01%) GC percentage = 43.76% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 25,946 number of insertions = 424 mapped reads with insertion percentage = 0.56% number of deletions = 1,252 mapped reads with deletion percentage = 1.69% homopolymer indels = 44.39% >>>>>>> Coverage mean coverageData = 0.0016X std coverageData = 0.0446X There is a 0.15% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 415843 0.0016683729746855877 0.05167683694346928 chr2 243199373 446302 0.0018351280864527559 0.055131981442739085 chr3 198022430 323571 0.0016340118642115442 0.04210087901820544 chr4 191154276 332728 0.0017406254621267275 0.04402114738456182 chr5 180915260 295399 0.0016328031145631387 0.04230529971643494 chr6 171115067 296265 0.0017313788037145788 0.043437275274404316 chr7 159138663 265381 0.0016676085810774972 0.04406403039057574 chr8 146364022 260413 0.0017792145668147873 0.04473403551077857 chr9 141213431 217332 0.0015390320769134206 0.04225477469746785 chr10 135534747 241842 0.0017843542364822506 0.047150270285192655 chr11 135006516 237976 0.0017627001055267584 0.04490662888605695 chr12 133851895 231308 0.0017280890942933606 0.04305281310291006 chr13 115169878 156916 0.0013624743094717874 0.03816905830024001 chr14 107349540 153920 0.0014338207690503379 0.03994363130034574 chr15 102531392 148858 0.0014518285287690232 0.03954558607546834 chr16 90354753 149432 0.0016538366277200713 0.046868352660136024 chr17 81195210 136519 0.0016813676570329704 0.04297145513012453 chr18 78077248 139060 0.00178105662740572 0.04704111392093211 chr19 59128983 104887 0.0017738678170737352 0.049135349934539954 chr20 63025520 102647 0.0016286577246804152 0.042200857919749694 chr21 48129895 68065 0.0014141938186235394 0.039515815776917915 chr22 51304566 64556 0.0012582895643245477 0.03744272138084202 chrMT 16571 4358 0.26298956007482954 0.5650007488391118 chrX 155270560 152616 9.829036489595968E-4 0.0329000672013145 chrY 59373566 50478 8.50176322574258E-4 0.043927015554384684