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Table 1 EFDR (homozygotes called heterozygotes) in blocks of 10 SNP using HMM-ASE and HMM-NASE

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

( λ , LD)   Number of individuals
   6 12 24
(8,0.5) ASE 0.0167 (0.017) 0.0117 (0.010) 0.0308 (0.020)
  NASE 0.0033 (0.007) 0.0050 (0.006) 0.0071 (0.004)
(8,0.8) ASE 0.0000 (0.000) 0.0150 (0.007) 0.0133 (0.005)
  NASE 0.0017 (0.005) 0.0050 (0.006) 0.0029 (0.004)
(16,0.5) ASE 0.0100 (0.009) 0.0000 (0.000) 0.0058 (0.004)
  NASE 0.0017 (0.005) 0.0008 (0.003) 0.0000 (0.000)
(16,0.8) ASE 0.0033 (0.008) 0.0017 (0.004) 0.0033 (0.004)
  NASE 0.0000 (0.000) 0.0008 (0.003) 0.0004 (0.001)
(24,0.5) ASE 0.0000 (0.000) 0.0033 (0.005) 0.0008 (0.002)
  NASE 0.0000 (0.000) 0.0000 (0.000) 0.0000 (0.000)
(24,0.8) ASE 0.0000 (0.000) 0.0000 (0.000) 0.0033 (0.004)
  NASE 0.0000 (0.000) 0.0000 (0.000) 0.0000 (0.000)
(32,0.5) ASE 0.0000 (0.000) 0.0000 (0.000) 0.0058 (0.006)
  NASE 0.0000 (0.000) 0.0000 (0.000) 0.0000 (0.000)
(32,0.8) ASE 0.0000 (0.000) 0.0017 (0.004) 0.0000 (0.000)
  NASE 0.0000 (0.000) 0.0000 (0.000) 0.0000 (0.000)
(56,0.5) ASE 0.0000 (0.000) 0.0000 (0.000) 0.0008 (0.002)
  NASE 0.0000 (0.000) 0.0000 (0.000) 0.0000 (0.000)
(56,0.8) ASE 0.0000 (0.000) 0.0000 (0.000) 0.0000 (0.000)
  NASE 0.0000 (0.000) 0.0000 (0.000) 0.0000 (0.000)
  1. Standard deviations are included in parenthesis.
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BMC Bioinformatics

ISSN: 1471-2105

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