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Simulated haplotype phasing by correlation of unique sequences within barcode-defined groups.

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posted on 2016-01-28, 12:38 authored by James A. Stapleton, Jeongwoon Kim, John P. Hamilton, Ming Wu, Luiz C. Irber, Rohan MaddamsettiRohan Maddamsetti, Bryan Briney, Linsey Newton, Dennis R. Burton, C. Titus BrownC. Titus Brown, Christina Chan, C. Robin Buell, Timothy A. Whitehead

Short unique sequences were identified at each end of the two variants (Env1_1 and Env1_2 from variant 1, Env2_1 and Env2_2 from variant 2). Each barcode-defined group of short reads was searched for the four sequences. A high number of counts of occurrences of a unique sequence from near the 5’ end of one env variant (Env1_1, Env2_1) in a barcode-defined group of short reads is a strong predictor of a high number of occurrences of a second unique sequence from the 3’ end of the same variant (Env1_2, Env2_2) in the same group, and also a strong predictor of a low number of occurrences of the unique sequence from the 3’ end of the other variant. Therefore, the haplotype across these two loci in a given barcoded individual can be phased regardless of the length or identity of the intervening sequence.

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