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Detailed information for vg0115180309:

Variant ID: vg0115180309 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 15180309
Reference Allele: T	Alternative Allele: C
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: 304. )

Flanking Sequence (100 bp) in Reference Genome:

TAATCTTCAAAGGATAATTTAGGAACAAAAATTTTTACACTGCACAAATCCATTCACCAGGAAGGCAAAGGGTACTGGGTACTCGAGCAGGTCGATCATG[T/C]
ACATTGACGAGACAATCAAAATCGATCGAACATCTTGAATGATCGCACTAACAGCAAGGCGGTCAATCTCATCTCAGGTTCGGATCATCAAATTGATCAG

Reverse complement sequence

CTGATCAATTTGATGATCCGAACCTGAGATGAGATTGACCGCCTTGCTGTTAGTGCGATCATTCAAGATGTTCGATCGATTTTGATTGTCTCGTCAATGT[A/G]
CATGATCGACCTGCTCGAGTACCCAGTACCCTTTGCCTTCCTGGTGAATGGATTTGTGCAGTGTAAAAATTTTTGTTCCTAAATTATCCTTTGAAGATTA

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	66.90%	33.00%	0.13%	0.00%	NA
All Indica	2759	95.60%	4.20%	0.18%	0.00%	NA
All Japonica	1512	14.70%	85.30%	0.00%	0.00%	NA
Aus	269	73.20%	26.80%	0.00%	0.00%	NA
Indica I	595	99.00%	0.80%	0.17%	0.00%	NA
Indica II	465	95.90%	4.10%	0.00%	0.00%	NA
Indica III	913	95.10%	4.80%	0.11%	0.00%	NA
Indica Intermediate	786	93.50%	6.10%	0.38%	0.00%	NA
Temperate Japonica	767	5.90%	94.10%	0.00%	0.00%	NA
Tropical Japonica	504	11.10%	88.90%	0.00%	0.00%	NA
Japonica Intermediate	241	50.60%	49.40%	0.00%	0.00%	NA
VI/Aromatic	96	62.50%	37.50%	0.00%	0.00%	NA
Intermediate	90	48.90%	50.00%	1.11%	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
vg0115180309	T -> C	LOC_Os01g27230.1	downstream_gene_variant ; 4767.0bp to feature; MODIFIER	silent_mutation	Average:58.223; most accessible tissue: Minghui63 flag leaf, score: 70.648	N	N	N	N
vg0115180309	T -> C	LOC_Os01g27210-LOC_Os01g27230	intergenic_region ; MODIFIER	silent_mutation	Average:58.223; most accessible tissue: Minghui63 flag leaf, score: 70.648	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0115180309	NA	6.83E-50	mr1519	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
vg0115180309	NA	2.57E-07	mr1690	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
vg0115180309	NA	1.91E-12	mr1744	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
vg0115180309	NA	8.26E-16	mr1950	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
vg0115180309	NA	2.30E-06	mr1064_2	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
vg0115180309	1.35E-09	8.63E-59	mr1519_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
vg0115180309	3.26E-07	1.39E-11	mr1519_2	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
vg0115180309	NA	1.22E-09	mr1705_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
vg0115180309	NA	9.90E-06	mr1745_2	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