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Detailed information for vg0113506305:

Variant ID: vg0113506305 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 13506305
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, T: 0.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

TTGGAGTCACGTTGCTTTCGTCGTCGGGAGCATTTTTCCGATTAATTTGGACAGCAAAAGCTACAAAATATCACTGCACACGATTGCTCAAATTACTGTG[C/T]
GTTACCTGTAGTTTTTTACACAATTATTTTGCATTAAAATCTGATGGACGCACATGAATCATTTCTTTTCAGTGGATACATCGCGCCCGAGTACTGCTCC

Reverse complement sequence

GGAGCAGTACTCGGGCGCGATGTATCCACTGAAAAGAAATGATTCATGTGCGTCCATCAGATTTTAATGCAAAATAATTGTGTAAAAAACTACAGGTAAC[G/A]
CACAGTAATTTGAGCAATCGTGTGCAGTGATATTTTGTAGCTTTTGCTGTCCAAATTAATCGGAAAAATGCTCCCGACGACGAAAGCAACGTGACTCCAA

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	86.20%	13.80%	0.00%	0.00%	NA
All Indica	2759	79.10%	20.90%	0.00%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	91.80%	8.20%	0.00%	0.00%	NA
Indica I	595	91.40%	8.60%	0.00%	0.00%	NA
Indica II	465	94.60%	5.40%	0.00%	0.00%	NA
Indica III	913	66.80%	33.20%	0.00%	0.00%	NA
Indica Intermediate	786	74.80%	25.20%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	54.20%	45.80%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0113506305	C -> T	LOC_Os01g23980.1	downstream_gene_variant ; 4069.0bp to feature; MODIFIER	silent_mutation	Average:59.23; most accessible tissue: Zhenshan97 root, score: 85.677	N	N	N	N
vg0113506305	C -> T	LOC_Os01g23990.1	downstream_gene_variant ; 2012.0bp to feature; MODIFIER	silent_mutation	Average:59.23; most accessible tissue: Zhenshan97 root, score: 85.677	N	N	N	N
vg0113506305	C -> T	LOC_Os01g23980-LOC_Os01g23990	intergenic_region ; MODIFIER	silent_mutation	Average:59.23; most accessible tissue: Zhenshan97 root, score: 85.677	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0113506305	NA	1.87E-06	mr1121	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
vg0113506305	NA	6.94E-09	mr1125	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
vg0113506305	NA	8.09E-08	mr1193	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
vg0113506305	5.63E-07	NA	mr1242	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
vg0113506305	2.39E-07	2.39E-07	mr1398	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
vg0113506305	NA	3.07E-10	mr1458	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
vg0113506305	NA	1.92E-06	mr1027_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
vg0113506305	NA	6.50E-10	mr1458_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
vg0113506305	NA	2.55E-06	mr1533_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