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Detailed information for vg1223982521:

Variant ID: vg1223982521 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23982521
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

TAAATATATATAGTGATGATCAGCTAGATAGACTAAAAGTACTCTAAAACCGATTATACTTATATATAAATTTGAAGTTAAAATTGTTCGTTTATATTTA[C/T]
GGACCGAGAGAGTAGCGATAAGAGTACTGCATAATTTGAAAGTGATCGATCGAACAAGCGATATATAGCATACGTACGGAGCACGTACGTAATGCATGCT

Reverse complement sequence

AGCATGCATTACGTACGTGCTCCGTACGTATGCTATATATCGCTTGTTCGATCGATCACTTTCAAATTATGCAGTACTCTTATCGCTACTCTCTCGGTCC[G/A]
TAAATATAAACGAACAATTTTAACTTCAAATTTATATATAAGTATAATCGGTTTTAGAGTACTTTTAGTCTATCTAGCTGATCATCACTATATATATTTA

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	64.00%	35.60%	0.44%	0.00%	NA
All Indica	2759	48.20%	51.40%	0.40%	0.00%	NA
All Japonica	1512	99.50%	0.40%	0.13%	0.00%	NA
Aus	269	11.90%	85.10%	2.97%	0.00%	NA
Indica I	595	52.60%	47.10%	0.34%	0.00%	NA
Indica II	465	70.30%	29.20%	0.43%	0.00%	NA
Indica III	913	33.00%	67.00%	0.00%	0.00%	NA
Indica Intermediate	786	49.50%	49.60%	0.89%	0.00%	NA
Temperate Japonica	767	99.60%	0.10%	0.26%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	76.70%	23.30%	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
vg1223982521	C -> T	LOC_Os12g39000.1	upstream_gene_variant ; 2700.0bp to feature; MODIFIER	silent_mutation	Average:49.507; most accessible tissue: Callus, score: 79.787	N	N	N	N
vg1223982521	C -> T	LOC_Os12g38990.1	downstream_gene_variant ; 734.0bp to feature; MODIFIER	silent_mutation	Average:49.507; most accessible tissue: Callus, score: 79.787	N	N	N	N
vg1223982521	C -> T	LOC_Os12g38990-LOC_Os12g39000	intergenic_region ; MODIFIER	silent_mutation	Average:49.507; most accessible tissue: Callus, score: 79.787	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1223982521	NA	1.53E-06	mr1571	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
vg1223982521	NA	2.34E-07	mr1928	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
vg1223982521	NA	1.94E-09	mr1928	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
vg1223982521	NA	4.32E-06	mr1931	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