BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084846.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 = 2,511,864 number of mapped reads = 2,193,726 (87.33%) number of supplementary alignments = 18,593 (0.74%) number of secondary alignments = 0 number of mapped bases = 152,055,969 bp number of sequenced bases = 151,995,568 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 109,357 duplication rate = 4.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.0668 >>>>>>> ACTG content number of A's = 44,456,275 bp (29.25%) number of C's = 27,953,876 bp (18.39%) number of T's = 48,741,900 bp (32.07%) number of G's = 30,819,011 bp (20.28%) number of N's = 24,506 bp (0.02%) GC percentage = 38.67% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,256,559 number of insertions = 12,831 mapped reads with insertion percentage = 0.58% number of deletions = 33,495 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.86% >>>>>>> Coverage mean coverageData = 0.0491X std coverageData = 0.4226X There is a 3.95% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% 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 11897308 0.04773231036403316 0.6212015834419369 chr2 243199373 13036246 0.05360312339292092 0.3890155098518725 chr3 198022430 10453763 0.052790802536864134 0.27330005601813817 chr4 191154276 11233786 0.058768164830380255 0.3040101782777641 chr5 180915260 9858701 0.05449347390596017 0.27943553718269304 chr6 171115067 9276620 0.05421275965137541 0.29026250987909846 chr7 159138663 8332957 0.05236286922933367 0.3312524449228258 chr8 146364022 7939117 0.05424227136912103 1.1044202380941541 chr9 141213431 6163828 0.04364902089235407 0.3430673802374497 chr10 135534747 6535190 0.04821781974477733 0.38596735321565084 chr11 135006516 7168950 0.05310077033615177 0.3438240243685179 chr12 133851895 6418608 0.04795306035824147 0.26226681082925796 chr13 115169878 5040316 0.04376418632656709 0.24869411613812956 chr14 107349540 4890222 0.045554196133490654 0.2615405790426733 chr15 102531392 4136517 0.04034390755174767 0.2378173871586958 chr16 90354753 3777105 0.04180305821875248 0.2654657131831519 chr17 81195210 3521060 0.04336536601112307 0.28330235664305 chr18 78077248 4356216 0.055793667317782514 0.6258916982029402 chr19 59128983 2325520 0.03932961268757151 0.4035850694193455 chr20 63025520 2964651 0.04703889789405942 0.26393106232509533 chr21 48129895 2008433 0.04172942824828519 0.2609162653719977 chr22 51304566 1404603 0.02737773865975204 0.19282222901460178 chrMT 16571 162972 9.834771588920404 5.380605743904248 chrX 155270560 8789274 0.056606184713959944 0.3047938743115722 chrY 59373566 364006 0.006130775436328012 0.15241529732842093