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SNPs were not analyzed because the reference genome did not come from the same strain.
In these instances, the repeated fragments were mapped uniquely because the reference genome does not capture their repetitive nature.
Unfortunately, because the reference genome is also from a laboratory-derived inbred strain, this study is not well suited to detect such deletions.
The strategies for model species are not feasible in wheat because the reference genome sequence and gene annotation of wheat remain incomplete.
VCGDB is "virtual" because the reference genome provided in the database is the statistical result of terabases of sequencing data from hundreds of Chinese individuals that describe the genetic variation features specific to the Chinese population.
As alluded to above we have also found that genes can be misannotated as pseudogenes because the reference genome has carried inactivating mutations that are not present in other alleles.
Similar(51)
We were unable to confirm the presence of genomic islands in our analysis because of the reference genome based tiling exercise employed to separate the subset of scaffolds potentially encoding the core genome and accessory genomes.
However, this is largely because the reference genomes include a closely related species ATCC29413.
This could happen because of gaps in the reference genome [ 3].
By contrast, we allow some vertices and edges to be ignored because some portions of the reference genome might not appear in the target genome.
To correct for this bias, each frequency bin (the proportion of strains in which the duplication was detected) was divided by 1− P, where P is the probability that a duplication at frequency P is undetectable because it is in the reference genome (Emerson et al. 2008; Schrider and Hahn 2010).
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because the barley genome
because the plastid genome
because the reference level
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because the zebrafish genome
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because the chimpanzee genome
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