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Detailed information for vg0103188289:

Variant ID: vg0103188289 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 3188289
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.72, T: 0.27, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

TTTACATGCGTAATCTGTAATTTATTTTGTTATTAGTCTACGTTTAATACTTCAAATGTGTGTTTGTATACTTCAAACTTAGGCTGTGTTTAGTTCACGC[T/C]
AAAATTGAAAGTTTGGTTGAAATTGGAACGATGTGACGGAAAAGTTTAAAGTTTGTGTGTGTAGAAAAGTTTTGATGTGATGAAAAAGTTGAAAGTTTGA

Reverse complement sequence

TCAAACTTTCAACTTTTTCATCACATCAAAACTTTTCTACACACACAAACTTTAAACTTTTCCGTCACATCGTTCCAATTTCAACCAAACTTTCAATTTT[A/G]
GCGTGAACTAAACACAGCCTAAGTTTGAAGTATACAAACACACATTTGAAGTATTAAACGTAGACTAATAACAAAATAAATTACAGATTACGCATGTAAA

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	26.40%	14.80%	0.72%	58.06%	NA
All Indica	2759	4.30%	7.40%	0.91%	87.35%	NA
All Japonica	1512	72.20%	12.00%	0.40%	15.34%	NA
Aus	269	3.30%	89.60%	0.00%	7.06%	NA
Indica I	595	1.50%	4.00%	0.84%	93.61%	NA
Indica II	465	2.80%	7.50%	1.29%	88.39%	NA
Indica III	913	6.80%	10.00%	0.77%	82.48%	NA
Indica Intermediate	786	4.50%	7.00%	0.89%	87.66%	NA
Temperate Japonica	767	65.40%	17.30%	0.65%	16.56%	NA
Tropical Japonica	504	81.50%	3.00%	0.00%	15.48%	NA
Japonica Intermediate	241	74.30%	14.10%	0.41%	11.20%	NA
VI/Aromatic	96	1.00%	52.10%	0.00%	46.88%	NA
Intermediate	90	31.10%	23.30%	3.33%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0103188289	T -> DEL	N	N	silent_mutation	Average:11.591; most accessible tissue: Callus, score: 59.674	N	N	N	N
vg0103188289	T -> C	LOC_Os01g06730.1	downstream_gene_variant ; 2943.0bp to feature; MODIFIER	silent_mutation	Average:11.591; most accessible tissue: Callus, score: 59.674	N	N	N	N
vg0103188289	T -> C	LOC_Os01g06740.1	downstream_gene_variant ; 468.0bp to feature; MODIFIER	silent_mutation	Average:11.591; most accessible tissue: Callus, score: 59.674	N	N	N	N
vg0103188289	T -> C	LOC_Os01g06730-LOC_Os01g06740	intergenic_region ; MODIFIER	silent_mutation	Average:11.591; most accessible tissue: Callus, score: 59.674	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0103188289	NA	4.83E-09	mr1005	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
vg0103188289	NA	5.04E-06	mr1101	Jap_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
vg0103188289	8.74E-06	8.74E-06	mr1317	Jap_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
vg0103188289	8.77E-06	8.77E-06	mr1589	Jap_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
vg0103188289	2.79E-06	3.20E-07	mr1897	Jap_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
vg0103188289	NA	1.98E-08	mr1321_2	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
vg0103188289	NA	2.75E-07	mr1749_2	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