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Genotypes of bins for regions at the transitions between two different genotype blocks were set to missing data.
Adjacent bins of the same genotype across the entire RIL population were merged and transition between two different genotype bins was determined as a breakpoint.
Accumulating data have revealed the frequent existence of mosaic HBV genomes, which are generally considered to be the result of recombination between two different genotype strains.
Genotypes of bins for regions at the transitions between two different genotype blocks were set to missing data and imputed using R/qtl package function fill.geno with the "argmax" method [42].
Consecutive SNP sites with the same genotype were lumped into blocks, and a breakpoint was assumed at the transition between two different genotype blocks.
Genotypes of bins for regions at the transitions between two different genotype blocks were set to missing data and imputed using the R/qtl package [ 47].
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Suitable results were analyzed by unpaired t test for the comparison of mean differences between two different genotypes of similar age.
In some cases, we also present a direct comparison between two different genotypes.
The comparison in the same age group between two different genotypes (GFAP-Cre positive or negative) was carried out using Excel with the two-tail Student t-test with both equal and unequal variance.
The first six maps were obtained from three controlled crosses (pedigrees #1, #2, and #3 in supplementary fig. S1, Supplementary Material online) between three different genotypes: Corsica × Landes (C×L), Morocco × Landes (M×L), and Corsica × Morocco (C×M).
The differential regulation of genes from the functional category hormones could suggest the involvement of hormone signaling between the two different genotypes in a grafted plant.
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