BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549014.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 = 10,017,269 number of mapped reads = 8,688,647 (86.74%) number of secondary alignments = 0 number of mapped bases = 344,002,473 bp number of sequenced bases = 343,964,723 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 449,043 duplication rate = 4.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6634 >>>>>>> ACTG content number of A's = 100,941,326 bp (29.35%) number of C's = 70,135,295 bp (20.39%) number of T's = 102,150,177 bp (29.7%) number of G's = 70,724,589 bp (20.56%) number of N's = 13,336 bp (0%) GC percentage = 40.95% >>>>>>> Mismatches and indels general error rate = 0.0025 number of mismatches = 840,195 number of insertions = 10,399 mapped reads with insertion percentage = 0.12% number of deletions = 28,460 mapped reads with deletion percentage = 0.33% homopolymer indels = 42.75% >>>>>>> Coverage mean coverageData = 0.1111X std coverageData = 1.248X There is a 7.98% of reference with a coverageData >= 1X There is a 2.11% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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% 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 27004118 0.10834122656007344 1.091831356217887 chr2 243199373 28659398 0.11784322322245461 0.6042591782168233 chr3 198022430 23154371 0.11692802173975948 0.4495209471235693 chr4 191154276 22589008 0.11817160710545653 0.4666195059026293 chr5 180915260 21566473 0.11920759476011034 0.459708945576517 chr6 171115067 20481313 0.11969321789763844 0.5067453885856125 chr7 159138663 19032653 0.1195979194571969 0.8591781727779704 chr8 146364022 17850646 0.12196061406402182 5.001069754258879 chr9 141213431 14786507 0.1047103444430863 0.5640937824395981 chr10 135534747 15730635 0.116063484443587 0.5509790431189181 chr11 135006516 15666440 0.11604210273821154 0.7208395630402821 chr12 133851895 15691471 0.11723009973075092 0.4624625950768605 chr13 115169878 11477497 0.09965710825881052 0.41244305205174603 chr14 107349540 10716591 0.0998289419777672 0.4712116877510668 chr15 102531392 10038364 0.09790527373314116 0.4070548816584695 chr16 90354753 9397722 0.10400916042568342 0.45231362863852514 chr17 81195210 8618153 0.10614115044471219 0.46840383766232746 chr18 78077248 9353552 0.11979868962594584 0.9864971083785534 chr19 59128983 6350212 0.10739592798340536 0.9380169918017328 chr20 63025520 6786391 0.10767687438358303 0.4416701740188066 chr21 48129895 4522678 0.09396816677036175 0.444774282773905 chr22 51304566 3785461 0.07378409555204112 0.4237060564601092 chrMT 16571 19040 1.1489952326353268 1.623772738617558 chrX 155270560 19782979 0.12740972274460785 0.5645920352881191 chrY 59373566 940800 0.015845435323861127 0.2238522829232918