Table 1 Confusion matrices of simulated individuals’ proportional assignment with NEWHYBRIDS based on data from: (A) Top 300 Fst SNPs; (B) Top 600 Fst SNPs; (C) Random 350 SNPs from the top 600 Fst SNPs (Random 350 Fst); and (D) 342 final SNP panel.

From: Genotyping-in-Thousands by sequencing panel development and application for high-resolution monitoring of introgressive hybridization within sockeye salmon

A: Top 300 Fst

Kokanee

Sockeye

F1

F2

B2 Kokanee

B2 Sockeye

Kokanee

1.000

0.000

0.000

0.000

0.000

0.000

Sockeye

0.000

1.000

0.000

0.000

0.000

0.000

F1

0.000

0.000

1.000

0.000

0.000

0.000

F2

0.000

0.000

0.020

0.980

0.000

0.000

B2 Kokanee

0.000

0.000

0.000

0.000

1.000

0.000

B2 Sockeye

0.000

0.000

0.000

0.000

0.000

1.000

B: Top 600 Fst

Kokanee

Sockeye

F1

F2

B2 Kokanee

B2 Sockeye

Kokanee

1.000

0.000

0.000

0.000

0.000

0.000

Sockeye

0.000

1.000

0.000

0.000

0.000

0.000

F1

0.000

0.000

0.960

0.040

0.000

0.000

F2

0.000

0.000

0.020

0.980

0.000

0.000

B2 Kokanee

0.000

0.000

0.000

0.000

1.000

0.000

B2 Sockeye

0.000

0.000

0.000

0.000

0.000

1.000

C: Random 350 Fst

Kokanee

Sockeye

F1

F2

B2 Kokanee

B2 Sockeye

Kokanee

1.000

0.000

0.000

0.000

0.000

0.000

Sockeye

0.000

1.000

0.000

0.000

0.000

0.000

F1

0.000

0.000

0.970

0.030

0.000

0.000

F2

0.000

0.000

0.060

0.920

0.020

0.000

B2 Kokanee

0.000

0.000

0.000

0.000

1.000

0.000

B2 Sockeye

0.000

0.000

0.000

0.010

0.000

0.990

D: 342 Final

Kokanee

Sockeye

F1

F2

B2 Kokanee

B2 Sockeye

Kokanee

1.000

0.000

0.000

0.000

0.000

0.000

Sockeye

0.000

1.000

0.000

0.000

0.000

0.000

F1

0.000

0.000

0.950

0.050

0.000

0.000

F2

0.000

0.000

0.050

0.940

0.000

0.010

B2 Kokanee

0.000

0.000

0.010

0.020

0.970

0.000

B2 Sockeye

0.000

0.000

0.000

0.020

0.000

0.980

  1. Rows represent true genetic classification, with columns as assigned hybrid class. Bold values along the diagonal are correct assignment proportions. Subsets of candidate markers were tested for informativeness to assess potential primer dropout.