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Detailed information for vg1222410674:

Variant ID: vg1222410674 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22410674
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.81, C: 0.18, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:

GGCCTTTGAGCCCATGTAGCCCTTTGGTTCCATGGCGAAGGTGCTCCAAGCGGTCGCGAATCTTTCATGCTTCGCCCGGACGTTTCACCCAAAGTGAATG[T/C]
TTTGGTCCTCGCTTGGTTGCTTCGCCCTGGTCGCAGTGGTTTCGGCAGCCTCGATCGAAGGCCCTCGTGGCATGCCTCCAACAAGCTCACCCATTCTCCG

Reverse complement sequence

CGGAGAATGGGTGAGCTTGTTGGAGGCATGCCACGAGGGCCTTCGATCGAGGCTGCCGAAACCACTGCGACCAGGGCGAAGCAACCAAGCGAGGACCAAA[A/G]
CATTCACTTTGGGTGAAACGTCCGGGCGAAGCATGAAAGATTCGCGACCGCTTGGAGCACCTTCGCCATGGAACCAAAGGGCTACATGGGCTCAAAGGCC

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	38.20%	17.90%	0.61%	43.36%	NA
All Indica	2759	9.60%	29.40%	0.72%	60.35%	NA
All Japonica	1512	86.20%	0.70%	0.33%	12.83%	NA
Aus	269	32.30%	4.50%	0.74%	62.45%	NA
Indica I	595	10.80%	29.70%	0.84%	58.66%	NA
Indica II	465	4.50%	17.20%	1.29%	76.99%	NA
Indica III	913	9.90%	34.90%	0.33%	54.87%	NA
Indica Intermediate	786	11.30%	29.80%	0.76%	58.14%	NA
Temperate Japonica	767	91.30%	0.10%	0.26%	8.34%	NA
Tropical Japonica	504	77.20%	1.20%	0.60%	21.03%	NA
Japonica Intermediate	241	88.80%	1.20%	0.00%	9.96%	NA
VI/Aromatic	96	92.70%	2.10%	0.00%	5.21%	NA
Intermediate	90	66.70%	12.20%	2.22%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1222410674	T -> C	LOC_Os12g36600.1	upstream_gene_variant ; 3789.0bp to feature; MODIFIER	silent_mutation	Average:17.669; most accessible tissue: Callus, score: 43.408	N	N	N	N
vg1222410674	T -> C	LOC_Os12g36590.1	intron_variant ; MODIFIER	silent_mutation	Average:17.669; most accessible tissue: Callus, score: 43.408	N	N	N	N
vg1222410674	T -> DEL	N	N	silent_mutation	Average:17.669; most accessible tissue: Callus, score: 43.408	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222410674	NA	1.76E-06	mr1013	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
vg1222410674	NA	9.71E-06	mr1021	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
vg1222410674	NA	3.90E-07	mr1031	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
vg1222410674	NA	5.21E-06	mr1056	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
vg1222410674	NA	6.02E-06	mr1324	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
vg1222410674	NA	5.92E-06	mr1532	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
vg1222410674	NA	4.41E-08	mr1660	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
vg1222410674	NA	1.36E-06	mr1660	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
vg1222410674	4.45E-06	4.45E-06	mr1738	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