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Table 5 Matching of whole genome and RNA-Seq data from standard and minute hilum isolines

From: Overexpression of an ethylene-forming ACC oxidase (ACO) gene precedes the Minute Hilum seed coat phenotype in Glycine max

Isoline

UC7

UC413

Category Explanation

ii R T Mi g

ii R t mi G

Category

Variants

Glymas

Variants

Glymas

 

1

70,776

14,740

100,613

16,146

Total mismatched variants & affected Glymas

2

2966

550

4108

607

Total within or near EH10 DEGs

3

244

103

275

115

Total within exons of EH10 DEGs

4

31

23

27

19

Indels within exons of EH10 DEGs

5

6

5

7

5

Indels within exons of EH10–25-50 DEGs

  1. Full data set of the 171,389 mismatched variants from the VCF file is shown in Additional file 12. Variants are those that differ at the same genome position number between UC7 and UC413. Thus, they do not include variants that differ from the reference genome but are identical in UC7 and UC413. Glymas are the number of unique Glymas found in the indicated set. Category explanations are found by successive filterings of the original VCF or expression data. DEGs, differentially expressed genes in stage EH10 or in all three stages EH10, EH25, and EH50 at padj < 0.05