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Old 03-23-2016, 06:04 PM   #1
gongyh211
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Location: china

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Smile What's happening about my kmer spectrum? Heterozygous or repeats?

I am doing a denovo genome sequencing and i get the kmer spectrum using clean reads of two paired end libarary data(see attach files). From the plot, i see high sequencing bias and two peaks, but i can not know whether the first peak(highest) is homozygous peak or heterozygous peak, the two situation are quite different. Whether the second peak (2X peak) is from large fragment duplication? or the first peak is heterozygous peak?
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Old 03-24-2016, 11:43 AM   #2
westerman
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It is difficult to differentiate between zygosity effects and duplications. In part it depends on the type of organism you are sequencing. Plants are notorious for duplications but then it can be easy to breed them to be homozygous. So a bit more information would be appreciated.
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Old 03-24-2016, 05:38 PM   #3
gongyh211
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Quote:
Originally Posted by westerman View Post
It is difficult to differentiate between zygosity effects and duplications. In part it depends on the type of organism you are sequencing. Plants are notorious for duplications but then it can be easy to breed them to be homozygous. So a bit more information would be appreciated.
Thank you Westerman. What i am sequencing is a green algae probably diploid but we didnot have direct evidence.
From the kmer spectrum, if the first mean peak is heterozygous peak, then it is so serious. I extracted the longest scaffold and two chloroplast scaffolds from the draft assembly, it shows 1.6%,2.1%,3.1% SNP (i use a simple ciritera: base coverage>=5 and highest nuc > 80%). It is very puzzled (chloroplast SNP>nuclear genome SNP?). One paper sequenced the chloroplast genome but very fragment(the author's explanation is repeats).
Do you know why Dunaliella salina still not public one usable version from JGI? Our algae is near to Dunaliella salina from phylogenetic tree.
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denovo assembly, heterozygous, kmer frequency histogram, kmer genome size, repeats

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