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Detailed information for vg0224428620:

Variant ID: vg0224428620 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24428620
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

TCGAGCTGAGAAATGGACCACTGACGAATAGAGGCAACAGCTAACAGGGTCCGAATGGTGGTCATGTGAGCAACTGGAGCAAAAGTCTCACCATAGTCAC[G/A]
ACCATGCTCTTGCTGAAAACCACGAGCTACAAGACGAGCTTTGTACCGCTCAAGAGAGCCATCAGAGCGAGTCTTTATCTTGTAGACCCACTTACAAGTG

Reverse complement sequence

CACTTGTAAGTGGGTCTACAAGATAAAGACTCGCTCTGATGGCTCTCTTGAGCGGTACAAAGCTCGTCTTGTAGCTCGTGGTTTTCAGCAAGAGCATGGT[C/T]
GTGACTATGGTGAGACTTTTGCTCCAGTTGCTCACATGACCACCATTCGGACCCTGTTAGCTGTTGCCTCTATTCGTCAGTGGTCCATTTCTCAGCTCGA

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%	7.90%	1.44%	27.42%	NA
All Indica	2759	84.50%	13.40%	0.43%	1.67%	NA
All Japonica	1512	22.20%	0.10%	2.91%	74.80%	NA
Aus	269	86.20%	0.00%	0.74%	13.01%	NA
Indica I	595	95.10%	1.80%	0.50%	2.52%	NA
Indica II	465	98.10%	1.10%	0.22%	0.65%	NA
Indica III	913	70.50%	28.60%	0.00%	0.88%	NA
Indica Intermediate	786	84.70%	11.70%	1.02%	2.54%	NA
Temperate Japonica	767	21.60%	0.00%	3.26%	75.10%	NA
Tropical Japonica	504	23.00%	0.20%	1.98%	74.80%	NA
Japonica Intermediate	241	22.40%	0.00%	3.73%	73.86%	NA
VI/Aromatic	96	29.20%	1.00%	10.42%	59.38%	NA
Intermediate	90	68.90%	1.10%	0.00%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0224428620	G -> A	LOC_Os02g40340.1	downstream_gene_variant ; 3431.0bp to feature; MODIFIER	silent_mutation	Average:14.502; most accessible tissue: Minghui63 root, score: 33.152	N	N	N	N
vg0224428620	G -> A	LOC_Os02g40340.2	downstream_gene_variant ; 3435.0bp to feature; MODIFIER	silent_mutation	Average:14.502; most accessible tissue: Minghui63 root, score: 33.152	N	N	N	N
vg0224428620	G -> A	LOC_Os02g40330-LOC_Os02g40340	intergenic_region ; MODIFIER	silent_mutation	Average:14.502; most accessible tissue: Minghui63 root, score: 33.152	N	N	N	N
vg0224428620	G -> DEL	N	N	silent_mutation	Average:14.502; most accessible tissue: Minghui63 root, score: 33.152	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224428620	4.24E-06	NA	mr1275	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
vg0224428620	3.80E-06	1.09E-06	mr1392	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