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Detailed information for vg0210325233:

Variant ID: vg0210325233 (JBrowse)	Variation Type: INDEL
Chromosome: chr02	Position: 10325233
Reference Allele: G	Alternative Allele: A,GGT
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.77, A: 0.24, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

CACTATGAGAAATACTTTCATGATATATGTCGACGGGTGATACCCGTAGACCGGATGAATAGGGTATTGGGGTACGTTGGAACAGGGATCTGCGCAATAC[G/A,GGT]
ACACCAAGCAAGCAAAGAGACAAGGATTATACTGGTTTAGGTCTCTTATCAGGTAATAGCCATAGTCCAATTTATTTGGGATTGATATGGAAAAACCATA

Reverse complement sequence

TATGGTTTTTCCATATCAATCCCAAATAAATTGGACTATGGCTATTACCTGATAAGAGACCTAAACCAGTATAATCCTTGTCTCTTTGCTTGCTTGGTGT[C/T,ACC]
GTATTGCGCAGATCCCTGTTCCAACGTACCCCAATACCCTATTCATCCGGTCTACGGGTATCACCCGTCGACATATATCATGAAAGTATTTCTCATAGTG

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	78.30%	21.60%	0.13%	0.00%	NA
All Indica	2759	69.70%	30.10%	0.18%	0.00%	NA
All Japonica	1512	99.40%	0.50%	0.07%	0.00%	NA
Aus	269	41.30%	58.70%	0.00%	0.00%	NA
Indica I	595	67.60%	32.30%	0.17%	0.00%	NA
Indica II	465	85.20%	14.80%	0.00%	0.00%	NA
Indica III	913	61.90%	38.00%	0.11%	0.00%	NA
Indica Intermediate	786	71.20%	28.40%	0.38%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	98.40%	1.40%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	85.60%	14.40%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0210325233	G -> A	LOC_Os02g17840-LOC_Os02g17850	intergenic_region ; MODIFIER	silent_mutation	Average:49.344; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg0210325233	G -> GGT	LOC_Os02g17840-LOC_Os02g17850	intergenic_region ; MODIFIER	N	Average:49.344; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0210325233	NA	2.06E-07	mr1245	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
vg0210325233	1.84E-06	1.84E-06	mr1460	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