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Detailed information for vg0808232376:

Variant ID: vg0808232376 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8232376
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

TTACTTTTAGAAGTTCCGAACCTTTAAAAATTGAACCATGTAGTTTTTAGAGTTTATTGTCTTGTTGGGTTTTATTTTTTATAATTTTTAGAAGTCTCGT[C/T]
AAACGATGCCACTGTGCTCCTCTACGGCCCGTCCACCGCCTACTCTTTATTGTCATTGTGATTCTAAAAATTGAACATAACTATCGTTGGAATTCATTTT

Reverse complement sequence

AAAATGAATTCCAACGATAGTTATGTTCAATTTTTAGAATCACAATGACAATAAAGAGTAGGCGGTGGACGGGCCGTAGAGGAGCACAGTGGCATCGTTT[G/A]
ACGAGACTTCTAAAAATTATAAAAAATAAAACCCAACAAGACAATAAACTCTAAAAACTACATGGTTCAATTTTTAAAGGTTCGGAACTTCTAAAAGTAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.70%	5.80%	9.39%	34.13%	NA
All Indica	2759	26.40%	9.40%	13.81%	50.42%	NA
All Japonica	1512	91.60%	0.30%	1.72%	6.35%	NA
Aus	269	58.40%	1.90%	5.20%	34.57%	NA
Indica I	595	17.00%	12.30%	13.95%	56.81%	NA
Indica II	465	23.70%	4.50%	6.88%	64.95%	NA
Indica III	913	34.40%	12.50%	17.96%	35.16%	NA
Indica Intermediate	786	25.70%	6.60%	12.98%	54.71%	NA
Temperate Japonica	767	95.40%	0.00%	0.52%	4.04%	NA
Tropical Japonica	504	93.80%	0.40%	2.18%	3.57%	NA
Japonica Intermediate	241	74.70%	1.20%	4.56%	19.50%	NA
VI/Aromatic	96	85.40%	0.00%	8.33%	6.25%	NA
Intermediate	90	51.10%	2.20%	16.67%	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
vg0808232376	C -> T	LOC_Os08g13800.1	intron_variant ; MODIFIER	silent_mutation	Average:12.821; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0808232376	C -> DEL	N	N	silent_mutation	Average:12.821; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808232376	1.68E-06	1.69E-06	mr1447	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
vg0808232376	1.11E-06	1.11E-06	mr1447	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