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Detailed information for vg0224385108:

Variant ID: vg0224385108 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24385108
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.78, A: 0.22, others allele: 0.00, population size: 27. )

Flanking Sequence (100 bp) in Reference Genome:

GGAGGAGTACAATGGCAAAGCCGCTGATCGTTTGGCGAGACATCTAGAAAGTAAAAAAAATGAACCTAAACAATAATTTTGTTCATTTTAAGACCCCAAT[A/G]
ACAATAAAGAAGGGGCAGCGGACGGGTCATAGAGGCAGCGTTTGACCGTACTTCTAAAAATTATAAAAATGAAAACCAACAAAACAATAAACTCTAAAAA

Reverse complement sequence

TTTTTAGAGTTTATTGTTTTGTTGGTTTTCATTTTTATAATTTTTAGAAGTACGGTCAAACGCTGCCTCTATGACCCGTCCGCTGCCCCTTCTTTATTGT[T/C]
ATTGGGGTCTTAAAATGAACAAAATTATTGTTTAGGTTCATTTTTTTTACTTTCTAGATGTCTCGCCAAACGATCAGCGGCTTTGCCATTGTACTCCTCC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.30%	12.30%	0.30%	24.06%	NA
All Indica	2759	67.40%	10.90%	0.36%	21.35%	NA
All Japonica	1512	54.30%	16.40%	0.26%	29.03%	NA
Aus	269	76.60%	4.80%	0.00%	18.59%	NA
Indica I	595	43.20%	10.60%	1.18%	45.04%	NA
Indica II	465	86.20%	5.40%	0.00%	8.39%	NA
Indica III	913	67.50%	14.00%	0.11%	18.40%	NA
Indica Intermediate	786	74.60%	10.70%	0.25%	14.50%	NA
Temperate Japonica	767	43.90%	20.10%	0.13%	35.85%	NA
Tropical Japonica	504	74.60%	13.30%	0.20%	11.90%	NA
Japonica Intermediate	241	44.80%	11.20%	0.83%	43.15%	NA
VI/Aromatic	96	46.90%	10.40%	0.00%	42.71%	NA
Intermediate	90	67.80%	12.20%	0.00%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0224385108	A -> G	LOC_Os02g40270.1	upstream_gene_variant ; 2435.0bp to feature; MODIFIER	silent_mutation	Average:22.119; most accessible tissue: Minghui63 root, score: 43.505	N	N	N	N
vg0224385108	A -> G	LOC_Os02g40270-LOC_Os02g40280	intergenic_region ; MODIFIER	silent_mutation	Average:22.119; most accessible tissue: Minghui63 root, score: 43.505	N	N	N	N
vg0224385108	A -> DEL	N	N	silent_mutation	Average:22.119; most accessible tissue: Minghui63 root, score: 43.505	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224385108	5.98E-06	NA	mr1083	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0224385108	2.32E-06	NA	mr1253	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251