BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081906.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 = 2,782,661 number of mapped reads = 2,582,114 (92.79%) number of supplementary alignments = 19,356 (0.7%) number of secondary alignments = 0 number of mapped bases = 177,689,554 bp number of sequenced bases = 177,626,149 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,760 duplication rate = 2.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0178 >>>>>>> ACTG content number of A's = 51,356,179 bp (28.91%) number of C's = 33,512,347 bp (18.87%) number of T's = 55,344,648 bp (31.16%) number of G's = 37,410,907 bp (21.06%) number of N's = 2,068 bp (0%) GC percentage = 39.93% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,413,112 number of insertions = 12,874 mapped reads with insertion percentage = 0.49% number of deletions = 35,571 mapped reads with deletion percentage = 1.36% homopolymer indels = 47.18% >>>>>>> Coverage mean coverageData = 0.0574X std coverageData = 0.4504X There is a 4.83% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.11% 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 12556216 0.050375866465744934 0.8397086495451845 chr2 243199373 15337087 0.06306384268515364 0.5023440198021432 chr3 198022430 10996428 0.05553122441735515 0.27136720468512937 chr4 191154276 12792695 0.06692340484185663 0.3208622398300563 chr5 180915260 11469588 0.0633975707742951 0.28958986945727977 chr6 171115067 9473600 0.0553639148561944 0.30536853052863616 chr7 159138663 9536365 0.05992487821768366 0.506023155473653 chr8 146364022 9335691 0.06378405616648058 0.6613263199000489 chr9 141213431 7040649 0.04985821072501241 0.39500920675339957 chr10 135534747 9764413 0.0720436140261508 0.5186814505789569 chr11 135006516 8701383 0.06445157802605617 0.3826774227576488 chr12 133851895 7598414 0.05676732481075445 0.2743005438778138 chr13 115169878 5693560 0.04943619025106547 0.25239091754586085 chr14 107349540 5210648 0.04853908083816661 0.2686529487162397 chr15 102531392 4520898 0.04409281793423813 0.24231864661178182 chr16 90354753 5610262 0.06209149838525927 0.34110348501790605 chr17 81195210 4117289 0.050708520859789635 0.2884793168496223 chr18 78077248 4774682 0.06115330806741549 0.6924553435286183 chr19 59128983 3058533 0.05172646043988276 0.6373629060490421 chr20 63025520 3546908 0.056277330198941634 0.27737430802775853 chr21 48129895 2311378 0.048023749064900305 0.278285263834638 chr22 51304566 1773682 0.034571620779327905 0.21016842873351574 chrMT 16571 4653 0.28079174461408485 0.6158290586713108 chrX 155270560 11994395 0.07724835281073245 0.35272995017122327 chrY 59373566 470137 0.007918288081264985 0.17875539782453334