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Figure 1 | Genome Biology

Figure 1

From: Assembly of a phased diploid Candida albicansgenome facilitates allele-specific measurements and provides a simple model for repeat and indel structure

Figure 1

Sequencing of strains that contain homozygous regions can resolve genome phasing. (A) Schematic illustrating the ambiguous phasing of two adjacent SNPs from chromosome 3 of C. albicans genome Assembly 21. (B) Idealized panel of strains to resolve phasing. The wild-type (WT) strain is heterozygous for all eight chromosomes, having both the A homolog in green, and the B homolog in blue. Additional strains to sequence were selected to be homozygous for the indicated chromosomes. (C) One phasing option from (A) can be excluded by sequencing the ‘3AA’ strain, since all reads are effectively from the A allele, pairing the T and C; SNPs on the B allele are inferred. (D) Illustration of how to calculate the max-to-sum ratio, with a SNP position highlighted in orange. (E, F) Histograms of max-to-sum ratios for all positions across chromosome 5 in wild type (E) and the ‘5AA’ strain (F); bars are in linear space, and the line plot is in log space.

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Genome Biology

ISSN: 1474-760X

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