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Detailed information for vg1123105257:

Variant ID: vg1123105257 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23105257
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.06, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

AAGTAATTATTAATTTTTTTCCTATCATTTGATTCATTGTTAAATATATTTTTATGTAGGCATATAATTTTACATATTTCACAAAAGTTTTTGAATAAGA[C/T]
GAACGGTTAAACATGCGCTAAAAAGTCAACGGTGTCAAACATTTCGAAACGGAGGGAGTATTAATCATGCATGCCTGATGAATTACACGTTGCCATTTTG

Reverse complement sequence

CAAAATGGCAACGTGTAATTCATCAGGCATGCATGATTAATACTCCCTCCGTTTCGAAATGTTTGACACCGTTGACTTTTTAGCGCATGTTTAACCGTTC[G/A]
TCTTATTCAAAAACTTTTGTGAAATATGTAAAATTATATGCCTACATAAAAATATATTTAACAATGAATCAAATGATAGGAAAAAAATTAATAATTACTT

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	78.10%	20.60%	0.06%	1.25%	NA
All Indica	2759	71.10%	28.90%	0.04%	0.00%	NA
All Japonica	1512	89.60%	6.40%	0.13%	3.90%	NA
Aus	269	77.00%	23.00%	0.00%	0.00%	NA
Indica I	595	89.10%	10.90%	0.00%	0.00%	NA
Indica II	465	38.70%	61.10%	0.22%	0.00%	NA
Indica III	913	81.20%	18.80%	0.00%	0.00%	NA
Indica Intermediate	786	65.00%	35.00%	0.00%	0.00%	NA
Temperate Japonica	767	98.70%	0.40%	0.13%	0.78%	NA
Tropical Japonica	504	80.60%	15.70%	0.00%	3.77%	NA
Japonica Intermediate	241	79.30%	6.20%	0.41%	14.11%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	77.80%	22.20%	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
vg1123105257	C -> T	LOC_Os11g38840.1	upstream_gene_variant ; 464.0bp to feature; MODIFIER	silent_mutation	Average:23.891; most accessible tissue: Callus, score: 50.161	N	N	N	N
vg1123105257	C -> T	LOC_Os11g38840-LOC_Os11g38850	intergenic_region ; MODIFIER	silent_mutation	Average:23.891; most accessible tissue: Callus, score: 50.161	N	N	N	N
vg1123105257	C -> DEL	N	N	silent_mutation	Average:23.891; most accessible tissue: Callus, score: 50.161	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123105257	NA	1.19E-06	mr1696	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
vg1123105257	NA	3.02E-07	mr1330_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
vg1123105257	4.02E-06	NA	mr1707_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