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Table 7 Contingency tables of genotype calling with five methods (columns) versus actual genotypes (rows)

From: A hidden Markov approach for ascertaining cSNP genotypes from RNA sequence data in the presence of allelic imbalance by exploiting linkage disequilibrium

Actual VarScan Genotype HMM-ASE HMM-NASE
genotype He Ho NC He Ho NC He Ho NC
       (Reads =0)    (Reads =0)
He 449 78 64 571 0 20 570 1 20
Ho 0 886 83 9 914 46 2 921 46
Actual SAMTOOLS + BCFTOOLS BEAGLE  
genotype He Ho NC He Ho NC    
He 576 9 6 583 8 0    
Ho 4 957 8 6 963 0    
  1. Values in bold represent counts of correct calls. The other values are incorrect calls or Non-called (NC).