BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080770.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 = 4,278,308 number of mapped reads = 3,128,569 (73.13%) number of supplementary alignments = 24,793 (0.58%) number of secondary alignments = 0 number of mapped bases = 200,112,652 bp number of sequenced bases = 200,048,640 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 351,920 duplication rate = 8.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9219 >>>>>>> ACTG content number of A's = 60,843,054 bp (30.41%) number of C's = 40,516,273 bp (20.25%) number of T's = 53,628,503 bp (26.81%) number of G's = 44,996,801 bp (22.49%) number of N's = 64,009 bp (0.03%) GC percentage = 42.75% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,486,234 number of insertions = 13,147 mapped reads with insertion percentage = 0.42% number of deletions = 35,153 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.99% >>>>>>> Coverage mean coverageData = 0.0646X std coverageData = 0.4067X There is a 4.42% of reference with a coverageData >= 1X There is a 1.22% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 24827014 0.09960662846252247 0.589552894471023 chr2 243199373 12199265 0.05016158080308867 0.33931570377806786 chr3 198022430 9827726 0.04962935764398003 0.3098204033475923 chr4 191154276 14851560 0.07769410295587634 0.4049913601679035 chr5 180915260 16461517 0.0909902072384607 0.4298245629481945 chr6 171115067 14237771 0.08320582897589024 0.49836152460232386 chr7 159138663 13756991 0.08644656641359366 0.5085773908935078 chr8 146364022 9491126 0.06484603162927567 0.4614352729854772 chr9 141213431 7131528 0.05050176848971257 0.3303725384392417 chr10 135534747 7532373 0.055575217180285144 0.36476651931996185 chr11 135006516 8772719 0.06497996733728023 0.38834653491968185 chr12 133851895 8626533 0.0644483441941558 0.3584946987517247 chr13 115169878 7855750 0.06821010959132907 0.3730348462600542 chr14 107349540 5256773 0.04896875198533687 0.3261326423053257 chr15 102531392 5601721 0.05463420412745396 0.33165900009147126 chr16 90354753 5398354 0.059746209477214776 0.3561407896581749 chr17 81195210 5947684 0.07325166102778723 0.39945798372424673 chr18 78077248 2854075 0.036554503048058254 0.3489593235480941 chr19 59128983 3829093 0.06475830981229629 0.5905057250471575 chr20 63025520 3773947 0.05987966461839585 0.3538520697881775 chr21 48129895 3327924 0.0691446345353548 0.3981438077533622 chr22 51304566 1306433 0.025464263746037732 0.22245337624129227 chrMT 16571 47280 2.853177237342345 3.0991903514488537 chrX 155270560 6797271 0.04377694651194663 0.29705465862702524 chrY 59373566 400224 0.006740777537262963 0.15040075118054255