BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085134.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 = 2,084,631 number of mapped reads = 1,885,437 (90.44%) number of supplementary alignments = 22,195 (1.06%) number of secondary alignments = 0 number of mapped bases = 126,490,587 bp number of sequenced bases = 126,442,849 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,770 duplication rate = 3.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8688 >>>>>>> ACTG content number of A's = 35,928,674 bp (28.41%) number of C's = 23,536,444 bp (18.61%) number of T's = 39,774,712 bp (31.46%) number of G's = 27,177,024 bp (21.49%) number of N's = 25,995 bp (0.02%) GC percentage = 40.11% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,137,503 number of insertions = 9,809 mapped reads with insertion percentage = 0.52% number of deletions = 29,726 mapped reads with deletion percentage = 1.56% homopolymer indels = 47.69% >>>>>>> Coverage mean coverageData = 0.0409X std coverageData = 0.3318X There is a 3.36% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.1% 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% 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 8797545 0.03529598026558176 0.46758368088222524 chr2 243199373 11069334 0.04551547096299463 0.3810603458099462 chr3 198022430 8551412 0.04318405748278112 0.24364561222354494 chr4 191154276 8509406 0.044515907140889696 0.25730449165733293 chr5 180915260 8317379 0.04597389407615477 0.25256974717175673 chr6 171115067 7654823 0.04473494435180275 0.2794466839832322 chr7 159138663 6266901 0.0393801285109452 0.3379312774808688 chr8 146364022 6922273 0.04729490830745277 0.640421600355255 chr9 141213431 5873809 0.0415952573236465 0.3054590570634197 chr10 135534747 5772728 0.04259223651334222 0.29501491281176356 chr11 135006516 5812204 0.04305128502093929 0.31706783340565253 chr12 133851895 5807266 0.04338575856546521 0.2468431025160892 chr13 115169878 4545682 0.039469365418621005 0.2358259595670639 chr14 107349540 3746443 0.03489947884266668 0.22806114348358406 chr15 102531392 3452870 0.03367622279038209 0.22042945151442847 chr16 90354753 3292362 0.03643817165877262 0.23529444707815692 chr17 81195210 3012268 0.03709908503223281 0.24209962092971568 chr18 78077248 3716463 0.0475998206289238 0.510323398100044 chr19 59128983 2139986 0.03619182829510191 0.3691769816130392 chr20 63025520 2395501 0.03800842896655196 0.23464247399183588 chr21 48129895 1694545 0.0352077435448384 0.23024787199753372 chr22 51304566 1278913 0.024927859247459574 0.18388611865225077 chrMT 16571 128274 7.740872608774365 4.847314681313868 chrX 155270560 7446667 0.0479592976286039 0.2747447751012258 chrY 59373566 285533 0.004809092989294259 0.1021802908329581