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Table 1 Detection procedure of presence/absence variation

From: Transcriptomic and presence/absence variation in the barley genome assessed from multi-tissue mRNA sequencing and their power to predict phenotypic traits

  

Expression

 

Expression

  

of gene

 

of ±5bp genic SNP

Tissue

t

1- β∗

α ∗

o

 

1- β∗

α ∗

o

Leaf&Seedling&Apex

1

45.0

88.8

88.6

 

64.2

90.8

85.3

 

2

34.6

87.5

81.8

 

53.0

90.1

81.8

 

3

30.1

86.7

79.5

 

44.8

90.0

79.5

 

4

25.1

87.0

77.3

 

38.4

89.8

77.3

 

5

21.4

86.5

77.3

 

32.7

89.7

77.3

Leaf&Seedling

2

35.2

87.5

81.8

 

52.4

90.3

79.5

Leaf

2

34.0

89.0

73.8

 

45.9

91.2

72.2

Seedling

2

28.1

86.7

76.7

 

45.9

90.5

76.2

  1. Statistical power (1−β∗) and the empirical type I error rate (α∗) to detect genomic presence/absence variation (gPAV) by expression PAV (ePAV), where t is the minimum number of inbreds that must have a present and absent call for a gene, o the percentage of common presence/absence values across all inbreds between ePAV and the genic PAV-SNP. We considered two scenarios: (i) the expression across the entire gene or (ii) the expression determined in a 10 bp window around the genic SNP was used to determine ePAV.
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BMC Genomics

ISSN: 1471-2164

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