BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818767.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 = 245,583 number of mapped reads = 235,059 (95.71%) number of supplementary alignments = 1,782 (0.73%) number of secondary alignments = 0 number of mapped bases = 15,949,114 bp number of sequenced bases = 15,942,583 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,823 duplication rate = 11.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9965 >>>>>>> ACTG content number of A's = 4,621,199 bp (28.99%) number of C's = 3,557,502 bp (22.31%) number of T's = 4,513,146 bp (28.31%) number of G's = 3,249,718 bp (20.38%) number of N's = 1,018 bp (0.01%) GC percentage = 42.7% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 81,150 number of insertions = 1,677 mapped reads with insertion percentage = 0.71% number of deletions = 4,042 mapped reads with deletion percentage = 1.7% homopolymer indels = 41% >>>>>>> Coverage mean coverageData = 0.0052X std coverageData = 0.093X There is a 0.43% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% 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 1342552 0.00538635368134148 0.11583333619007617 chr2 243199373 1393414 0.005729513126664187 0.11762443502021104 chr3 198022430 1076220 0.005434838871535916 0.08605347179949158 chr4 191154276 1041161 0.00544670525706681 0.08884582950711327 chr5 180915260 992114 0.0054838602337912235 0.08696147859073838 chr6 171115067 920296 0.0053782289083871265 0.08776627815394568 chr7 159138663 888445 0.005582835643152287 0.092169224170906 chr8 146364022 801899 0.005478798608034972 0.09042178307705186 chr9 141213431 684988 0.0048507283984906505 0.08519525596919678 chr10 135534747 764139 0.005637956442269376 0.09747409157173802 chr11 135006516 742842 0.005502267757209586 0.08910612524793407 chr12 133851895 727753 0.005437001844463988 0.08786168443840042 chr13 115169878 501478 0.004354246168429561 0.07716970286119942 chr14 107349540 525867 0.004898642323013214 0.08406709548228383 chr15 102531392 490422 0.00478313997726667 0.08111216604587518 chr16 90354753 474303 0.005249342001964191 0.10171070696987321 chr17 81195210 454804 0.005601364908102337 0.08924634278280665 chr18 78077248 420243 0.005382400260828865 0.09980245576410465 chr19 59128983 335122 0.005667643564916379 0.10734860934074252 chr20 63025520 342415 0.005432957951001436 0.08795388961775455 chr21 48129895 221154 0.0045949404211249574 0.08059108002301024 chr22 51304566 197208 0.003843868399549467 0.07548974495057546 chrMT 16571 9273 0.5595920584153038 0.9490089673275506 chrX 155270560 459955 0.0029622808084159677 0.06495694353781073 chrY 59373566 141047 0.0023755857952005104 0.09403884283122226