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Detailed information for vg0608925485:

Variant ID: vg0608925485 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 8925485
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: 104. )

Flanking Sequence (100 bp) in Reference Genome:

AGATTAAGTGTTTCACGCAAAACAAGGTTGTAATAACATGTGATTAATTGATTTTTAATTATTCCAAACTTAAAAAATAGATTAATATGATATTTTAGAA[C/T]
AACTTTCATATAGAAAGTTTTTGCACGAAACGCACCGTTTAGCAGTTTGAAAAGCGTACCATGAGTATCTAAAATTTAATCCAACTTTTATGGGGTTTAA

Reverse complement sequence

TTAAACCCCATAAAAGTTGGATTAAATTTTAGATACTCATGGTACGCTTTTCAAACTGCTAAACGGTGCGTTTCGTGCAAAAACTTTCTATATGAAAGTT[G/A]
TTCTAAAATATCATATTAATCTATTTTTTAAGTTTGGAATAATTAAAAATCAATTAATCACATGTTATTACAACCTTGTTTTGCGTGAAACACTTAATCT

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	49.50%	33.70%	1.69%	15.09%	NA
All Indica	2759	15.30%	56.30%	2.83%	25.59%	NA
All Japonica	1512	99.00%	0.70%	0.07%	0.20%	NA
Aus	269	99.30%	0.40%	0.00%	0.37%	NA
Indica I	595	8.10%	55.00%	5.55%	31.43%	NA
Indica II	465	20.40%	74.80%	0.43%	4.30%	NA
Indica III	913	16.30%	42.60%	2.52%	38.55%	NA
Indica Intermediate	786	16.50%	62.20%	2.54%	18.70%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.60%	0.00%	0.20%	NA
Japonica Intermediate	241	97.90%	0.80%	0.41%	0.83%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	65.60%	30.00%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0608925485	C -> T	LOC_Os06g15740.1	intron_variant ; MODIFIER	silent_mutation	Average:29.864; most accessible tissue: Callus, score: 65.898	N	N	N	N
vg0608925485	C -> DEL	N	N	silent_mutation	Average:29.864; most accessible tissue: Callus, score: 65.898	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0608925485	NA	1.02E-10	mr1946	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