BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081965.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 = 3,336,536 number of mapped reads = 3,022,517 (90.59%) number of supplementary alignments = 31,043 (0.93%) number of secondary alignments = 0 number of mapped bases = 201,690,685 bp number of sequenced bases = 201,619,007 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 175,287 duplication rate = 4.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0759 >>>>>>> ACTG content number of A's = 56,980,900 bp (28.26%) number of C's = 37,375,478 bp (18.54%) number of T's = 63,549,660 bp (31.52%) number of G's = 43,688,296 bp (21.67%) number of N's = 24,673 bp (0.01%) GC percentage = 40.21% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,551,242 number of insertions = 14,081 mapped reads with insertion percentage = 0.46% number of deletions = 40,987 mapped reads with deletion percentage = 1.34% homopolymer indels = 48.08% >>>>>>> Coverage mean coverageData = 0.0652X std coverageData = 0.4688X There is a 5.24% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 19155951 0.07685417562109104 0.7532206589516424 chr2 243199373 17966478 0.07387551118398648 0.6261058270623274 chr3 198022430 12810604 0.06469269163094302 0.30206101897261795 chr4 191154276 10545931 0.05516973630241993 0.28776546688693605 chr5 180915260 10560493 0.05837259388732603 0.2889406548455515 chr6 171115067 18071535 0.10561042529352485 0.4901038591332181 chr7 159138663 12212779 0.0767430036784964 0.5885610998027803 chr8 146364022 12077356 0.08251587948300573 0.7095341900627972 chr9 141213431 10082284 0.07139748626318697 0.4867169335267516 chr10 135534747 8089704 0.0596873066063273 0.4267830358656134 chr11 135006516 9023921 0.06684063308470237 0.37873417272374477 chr12 133851895 9060798 0.06769271365190609 0.3185776290577115 chr13 115169878 5679300 0.04931237315368173 0.2680390374978914 chr14 107349540 5463615 0.050895560428111754 0.2911578415770511 chr15 102531392 4848282 0.04728583027527803 0.2654312287143835 chr16 90354753 4619047 0.05112123985331463 0.29464426420911677 chr17 81195210 5556156 0.06842960317486708 0.3384289453502344 chr18 78077248 5883094 0.07534965884043454 0.7406790653189674 chr19 59128983 4457871 0.07539231648885285 0.5998813778413182 chr20 63025520 5264446 0.08352879912771842 0.35084262142512845 chr21 48129895 2354696 0.04892377180544441 0.2796256853433375 chr22 51304566 1625758 0.03168836863370016 0.2081392378337203 chrMT 16571 110105 6.6444390803210425 4.556815706587199 chrX 155270560 5817095 0.03746424950100006 0.2674518998839201 chrY 59373566 353386 0.005951907958501263 0.12668598818008628