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Detailed information for vg0625836722:

Variant ID: vg0625836722 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 25836722
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

CCAACCAACCACAAGAGAATGAGGACGAACGGCGATGTTTCTCTGATCCGATCCTGTACATGTATCAACGTATGTGACCTTGACCTAGCTAGGTCTTGAT[C/T]
ATTATCTCCCCTTTCTTTTTCTGTGTGGTGGTCTTGGGATGTTGGTCTTTCTTCTATGTTCTTTCACTGGATTGGTTTTTGACTTGAGAAAATTACAAAA

Reverse complement sequence

TTTTGTAATTTTCTCAAGTCAAAAACCAATCCAGTGAAAGAACATAGAAGAAAGACCAACATCCCAAGACCACCACACAGAAAAAGAAAGGGGAGATAAT[G/A]
ATCAAGACCTAGCTAGGTCAAGGTCACATACGTTGATACATGTACAGGATCGGATCAGAGAAACATCGCCGTTCGTCCTCATTCTCTTGTGGTTGGTTGG

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	85.40%	12.80%	1.76%	0.00%	NA
All Indica	2759	75.90%	21.20%	2.86%	0.00%	NA
All Japonica	1512	99.80%	0.10%	0.07%	0.00%	NA
Aus	269	99.30%	0.40%	0.37%	0.00%	NA
Indica I	595	82.20%	13.10%	4.71%	0.00%	NA
Indica II	465	89.00%	8.00%	3.01%	0.00%	NA
Indica III	913	72.40%	26.80%	0.77%	0.00%	NA
Indica Intermediate	786	67.40%	28.80%	3.82%	0.00%	NA
Temperate Japonica	767	99.60%	0.30%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	89.60%	9.40%	1.04%	0.00%	NA
Intermediate	90	90.00%	8.90%	1.11%	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
vg0625836722	C -> T	LOC_Os06g43000.1	3_prime_UTR_variant ; 79.0bp to feature; MODIFIER	silent_mutation	Average:60.515; most accessible tissue: Callus, score: 94.756	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0625836722	NA	3.22E-06	mr1060	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
vg0625836722	9.40E-06	7.38E-07	mr1378	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
vg0625836722	9.07E-06	9.07E-06	mr1703	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