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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