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To analyse relationships among plastid sequences in plastid haplotype networks, a consensus sequence of the large single copy plastid region was extracted for each of the 38 samples.

All detected false negatives were masked with Ns in the final consensus sequence.

Any combination of log likelihood ratio or coverage that placed variants in the grey box would be represented as a masked position in the final consensus sequence.

Any combination of log likelihood ratio or coverage that placed variants in the grey box would be represented as a masked position in the final consensus sequence.

All detected false negatives were masked with Ns in the final consensus sequence.