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Detailed information for vg0113805974:

Variant ID: vg0113805974 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 13805974
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.66, C: 0.34, others allele: 0.00, population size: 65. )

Flanking Sequence (100 bp) in Reference Genome:

TATCAAACAGGCACAACTTTGAGAACATTTCTTATGAGCCATGAAATTTGGTGGGGATTGTTAGAATAAATGGGCTAGACCCGATTTTTCTATTAAATCT[T/C]
AAGGGCCCATAATAAATGTTAAGGATAATAATACCACCCTGGGAATTAAACGAGGAGTATCTCAACTTAAATAGGGAGTTATTGGAGGCTCCCTGTTGAC

Reverse complement sequence

GTCAACAGGGAGCCTCCAATAACTCCCTATTTAAGTTGAGATACTCCTCGTTTAATTCCCAGGGTGGTATTATTATCCTTAACATTTATTATGGGCCCTT[A/G]
AGATTTAATAGAAAAATCGGGTCTAGCCCATTTATTCTAACAATCCCCACCAAATTTCATGGCTCATAAGAAATGTTCTCAAAGTTGTGCCTGTTTGATA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	34.00%	18.80%	7.05%	40.18%	NA
All Indica	2759	3.90%	21.40%	10.22%	64.48%	NA
All Japonica	1512	94.30%	3.00%	0.79%	1.85%	NA
Aus	269	1.10%	88.80%	2.23%	7.81%	NA
Indica I	595	2.40%	23.90%	9.58%	64.20%	NA
Indica II	465	3.70%	3.40%	10.97%	81.94%	NA
Indica III	913	6.40%	24.90%	9.53%	59.26%	NA
Indica Intermediate	786	2.30%	26.20%	11.07%	60.43%	NA
Temperate Japonica	767	97.00%	2.00%	0.13%	0.91%	NA
Tropical Japonica	504	88.90%	5.60%	1.98%	3.57%	NA
Japonica Intermediate	241	97.10%	1.20%	0.41%	1.24%	NA
VI/Aromatic	96	28.10%	1.00%	27.08%	43.75%	NA
Intermediate	90	48.90%	11.10%	7.78%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0113805974	T -> DEL	N	N	silent_mutation	Average:11.245; most accessible tissue: Callus, score: 26.054	N	N	N	N
vg0113805974	T -> C	LOC_Os01g24480.1	upstream_gene_variant ; 1184.0bp to feature; MODIFIER	silent_mutation	Average:11.245; most accessible tissue: Callus, score: 26.054	N	N	N	N
vg0113805974	T -> C	LOC_Os01g24490.1	downstream_gene_variant ; 1549.0bp to feature; MODIFIER	silent_mutation	Average:11.245; most accessible tissue: Callus, score: 26.054	N	N	N	N
vg0113805974	T -> C	LOC_Os01g24480-LOC_Os01g24490	intergenic_region ; MODIFIER	silent_mutation	Average:11.245; most accessible tissue: Callus, score: 26.054	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0113805974	2.41E-06	NA	mr1191	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
vg0113805974	NA	3.96E-06	mr1887	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