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Detailed information for vg0114463521:

Variant ID: vg0114463521 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14463521
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

GCGGGATCTGGTAGGGAGGCCGACGATGGATTTGGTAGGGAGGTACGCGGCGGAGTCGTGGTGAGGGGCGAGCGGTTGTTTGCGGCGAGGAGTTCGGCGG[C/T]
GATTGGCGAGAGCAAATAATTTTTCTTTTTCTTTGTTCTGTTTTCTCTAACCGATCAATCATTTGTAACCTGTCAAGTTGTAACCACCGGCTTAATACTG

Reverse complement sequence

CAGTATTAAGCCGGTGGTTACAACTTGACAGGTTACAAATGATTGATCGGTTAGAGAAAACAGAACAAAGAAAAAGAAAAATTATTTGCTCTCGCCAATC[G/A]
CCGCCGAACTCCTCGCCGCAAACAACCGCTCGCCCCTCACCACGACTCCGCCGCGTACCTCCCTACCAAATCCATCGTCGGCCTCCCTACCAGATCCCGC

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	94.50%	5.10%	0.11%	0.30%	NA
All Indica	2759	90.60%	8.70%	0.18%	0.51%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	93.80%	5.20%	0.67%	0.34%	NA
Indica II	465	92.70%	5.80%	0.22%	1.29%	NA
Indica III	913	91.10%	8.80%	0.00%	0.11%	NA
Indica Intermediate	786	86.40%	13.00%	0.00%	0.64%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0114463521	C -> T	LOC_Os01g25510.1	downstream_gene_variant ; 1672.0bp to feature; MODIFIER	silent_mutation	Average:57.492; most accessible tissue: Minghui63 young leaf, score: 70.655	N	N	N	N
vg0114463521	C -> T	LOC_Os01g25520.1	intron_variant ; MODIFIER	silent_mutation	Average:57.492; most accessible tissue: Minghui63 young leaf, score: 70.655	N	N	N	N
vg0114463521	C -> DEL	N	N	silent_mutation	Average:57.492; most accessible tissue: Minghui63 young leaf, score: 70.655	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114463521	1.33E-06	6.45E-06	mr1908	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