Hi, I annotated my VCF file with SNPEFF, but I was wondering why the codon change which is annotated by SNPEFF (SNPEFF_CODON_CHANGE=gaC/gaA) is not matching my reference (G) and alternative allele (A,T) in the VCF file. I copied part of the row below:

Chromosome  4482482 .   G         A,T   116681.74   PASS    AC=5,21;AF=0.051,0.212;AN=99;BaseQRankSum=0.045;DP=10649;
FS=0.000;MLEAC=5,21;MLEAF=0.051,0.212;MQ=60.00;MQRankSum=0.00;QD=31.58;ReadPosRankSum=-4.890e-01;
SNPEFF_AMINO_ACID_CHANGE=D452E;SNPEFF_CODON_CHANGE=gaC/gaA;
SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=1;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;
SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=valS;SNPEFF_IMPACT=MODERATE;
SNPEFF_TRANSCRIPT_ID=AAC77215;SOR=0.682 GT:AD:DP:GQ:PL  ...