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Detailed information for vg0104996735:

Variant ID: vg0104996735 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 4996735
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, G: 0.02, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

TAGTTCTCCTCACAAAAAAATAATTGTTAATATGGAAAAGATGATTATGATGTAATTAATGAGGATAGCAACGTAATTTGTCGCACCTCTTAGTTTAATA[T/G]
GAGATTCCCTAAAACGATAAGTAGATGGAAATAGATGGAATAGGATTTACCTTGTTATATGTTTCATAGCTTATTTCTCACTGATATATGAATCTTACGG

Reverse complement sequence

CCGTAAGATTCATATATCAGTGAGAAATAAGCTATGAAACATATAACAAGGTAAATCCTATTCCATCTATTTCCATCTACTTATCGTTTTAGGGAATCTC[A/C]
TATTAAACTAAGAGGTGCGACAAATTACGTTGCTATCCTCATTAATTACATCATAATCATCTTTTCCATATTAACAATTATTTTTTTGTGAGGAGAACTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.50%	48.20%	0.32%	0.00%	NA
All Indica	2759	79.60%	20.00%	0.36%	0.00%	NA
All Japonica	1512	1.00%	99.00%	0.00%	0.00%	NA
Aus	269	49.80%	49.10%	1.12%	0.00%	NA
Indica I	595	44.20%	55.30%	0.50%	0.00%	NA
Indica II	465	93.30%	6.50%	0.22%	0.00%	NA
Indica III	913	96.30%	3.60%	0.11%	0.00%	NA
Indica Intermediate	786	78.90%	20.50%	0.64%	0.00%	NA
Temperate Japonica	767	1.00%	99.00%	0.00%	0.00%	NA
Tropical Japonica	504	0.80%	99.20%	0.00%	0.00%	NA
Japonica Intermediate	241	1.20%	98.80%	0.00%	0.00%	NA
VI/Aromatic	96	46.90%	51.00%	2.08%	0.00%	NA
Intermediate	90	47.80%	52.20%	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
vg0104996735	T -> G	LOC_Os01g09690.1	downstream_gene_variant ; 2867.0bp to feature; MODIFIER	silent_mutation	Average:41.187; most accessible tissue: Callus, score: 80.512	N	N	N	N
vg0104996735	T -> G	LOC_Os01g09690-LOC_Os01g09700	intergenic_region ; MODIFIER	silent_mutation	Average:41.187; most accessible tissue: Callus, score: 80.512	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0104996735	NA	3.44E-12	mr1170	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
vg0104996735	NA	2.77E-09	mr1663	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
vg0104996735	NA	2.66E-06	mr1761	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
vg0104996735	7.50E-08	NA	mr1587_2	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
vg0104996735	1.34E-06	8.40E-06	mr1587_2	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