Fig. 2: Genotyping STRs in a triploid M. acuminata sample with a large duplication on chr02. | Communications Biology

Fig. 2: Genotyping STRs in a triploid M. acuminata sample with a large duplication on chr02.

From: Genotyping short tandem repeats across copy number alterations, aneuploidies, and polyploid organisms

Fig. 2

A Consistency of STR genotypes between the HiSeq1500 and NextSeq500 samples for different normalised depth filtering thresholds. X-axis: STR period, y-axis: proportion of loci for which the inferred genotype matched exactly between the two alignments. B Distributions of the depth of coverage for STR loci normalised by copy number for STRs in the alignment of combined HiSeq1500 and NextSeq500 reads. The blue distribution shows the normalised depths for loci not affected by CNAs. The orange distribution shows the normalised depth reported for loci in the chr02 duplication when CNA information was not provided to ConSTRain. The green distribution shows normalised depth for the loci in the chr02 duplication when CNA information was provided to ConSTRain. Vertical dashed lines indicate filtering bounds that exclude the 2.5% of loci with the highest and the 2.5% of loci with the lowest depth of coverage in the overall sample.

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