BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549106.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,601,805 number of mapped reads = 9,139,052 (86.2%) number of secondary alignments = 0 number of mapped bases = 363,048,021 bp number of sequenced bases = 363,014,518 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 393,158 duplication rate = 3.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.312 >>>>>>> ACTG content number of A's = 107,859,046 bp (29.71%) number of C's = 73,887,179 bp (20.35%) number of T's = 107,919,978 bp (29.73%) number of G's = 73,346,921 bp (20.2%) number of N's = 1,394 bp (0%) GC percentage = 40.56% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 1,077,193 number of insertions = 8,820 mapped reads with insertion percentage = 0.1% number of deletions = 26,611 mapped reads with deletion percentage = 0.29% homopolymer indels = 46.1% >>>>>>> Coverage mean coverageData = 0.1173X std coverageData = 0.7596X There is a 9.19% of reference with a coverageData >= 1X There is a 1.83% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 29832470 0.11968864863931472 1.625722056966621 chr2 243199373 31584593 0.12987119419917253 0.6410656435555775 chr3 198022430 25436894 0.12845460991464452 0.4348365138924924 chr4 191154276 25121908 0.13142216081004643 0.4794142056930284 chr5 180915260 22893417 0.12654221097766988 0.4450114586693895 chr6 171115067 21814603 0.12748499230637592 0.487904985530469 chr7 159138663 20553147 0.12915244235776946 1.039481671943442 chr8 146364022 19201705 0.13119142763103353 0.8900303583180013 chr9 141213431 15677348 0.11101881661667154 0.5920769921478816 chr10 135534747 17399466 0.12837642291094548 0.6776963502309119 chr11 135006516 17074687 0.1264730585300046 0.6189319155262367 chr12 133851895 16648823 0.12438242282636343 0.4535682049222686 chr13 115169878 12148886 0.1054866620593277 0.3898371425907229 chr14 107349540 11304733 0.10530769857048293 0.5082794983229274 chr15 102531392 10380978 0.10124682594770586 0.380561850162796 chr16 90354753 9628688 0.10656537348953851 0.4491633451318337 chr17 81195210 8743050 0.10767938157928282 0.4440602168830547 chr18 78077248 9742969 0.124786275766277 1.276305339844218 chr19 59128983 6153726 0.10407292139626349 1.2278065044524638 chr20 63025520 7354185 0.11668582821688739 0.45039763888995055 chr21 48129895 4953371 0.1029167215095732 0.4752101363291345 chr22 51304566 3795746 0.07398456503851919 0.34746494657042665 chrMT 16571 101532 6.127089493693802 8.005775608859075 chrX 155270560 12304509 0.07924560199950331 0.4502193441129272 chrY 59373566 3196587 0.053838555022954156 0.5174213463652576