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Fig. 3 | Genome Biology

Fig. 3

From: KAGE: fast alignment-free graph-based genotyping of SNPs and short indels

Fig. 3

Genotype accuracy increases when expected kmer counts are modelled from the population. Our prototype alignment-free genotyper (naive KAGE) performs a bit worse than Malva, as expected. However, when we compute expected kmer counts from the population, using 1000 Genomes data, and use these counts to compute the probability of observing the given kmers in our data, the genotyping accuracy greatly improves. Note: KAGE here refers to a simplified version of the full genotyper that we present in the next section (here KAGE does not use variants to adjust prior probabilities)

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