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Detailed information for vg1012827616:

Variant ID: vg1012827616 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 12827616
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.50, T: 0.50, others allele: 0.00, population size: 46. )

Flanking Sequence (100 bp) in Reference Genome:

TTCAAAAGTGAGAGAAGTTTTCTTTTGGATTTTCAAGCACGATGTGTACATTTGTACGAAGTGTGCTTTTTACCACTTTTGTTTTATTTTTTCCAAACAC[T/C]
AAAATATTTTTGATGGGTTTGCCAATGTGTTCATTGAGGGGGAGATTGTAAAATCAAAGGTGTTTTTGATTATTATTCTGTGATGAACAATTGGCATTGG

Reverse complement sequence

CCAATGCCAATTGTTCATCACAGAATAATAATCAAAAACACCTTTGATTTTACAATCTCCCCCTCAATGAACACATTGGCAAACCCATCAAAAATATTTT[A/G]
GTGTTTGGAAAAAATAAAACAAAAGTGGTAAAAAGCACACTTCGTACAAATGTACACATCGTGCTTGAAAATCCAAAAGAAAACTTCTCTCACTTTTGAA

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	32.60%	27.50%	0.95%	38.85%	NA
All Indica	2759	5.10%	32.30%	1.56%	60.96%	NA
All Japonica	1512	89.70%	1.40%	0.13%	8.73%	NA
Aus	269	0.40%	99.30%	0.00%	0.37%	NA
Indica I	595	10.40%	18.30%	2.52%	68.74%	NA
Indica II	465	4.90%	37.60%	1.08%	56.34%	NA
Indica III	913	1.50%	30.20%	0.99%	67.25%	NA
Indica Intermediate	786	5.50%	42.20%	1.78%	50.51%	NA
Temperate Japonica	767	96.90%	0.80%	0.00%	2.35%	NA
Tropical Japonica	504	83.10%	0.80%	0.20%	15.87%	NA
Japonica Intermediate	241	80.90%	4.60%	0.41%	14.11%	NA
VI/Aromatic	96	6.20%	91.70%	0.00%	2.08%	NA
Intermediate	90	41.10%	37.80%	0.00%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1012827616	T -> C	LOC_Os10g24910.1	downstream_gene_variant ; 1151.0bp to feature; MODIFIER	silent_mutation	Average:7.489; most accessible tissue: Callus, score: 26.506	N	N	N	N
vg1012827616	T -> C	LOC_Os10g24920.1	downstream_gene_variant ; 401.0bp to feature; MODIFIER	silent_mutation	Average:7.489; most accessible tissue: Callus, score: 26.506	N	N	N	N
vg1012827616	T -> C	LOC_Os10g24910-LOC_Os10g24920	intergenic_region ; MODIFIER	silent_mutation	Average:7.489; most accessible tissue: Callus, score: 26.506	N	N	N	N
vg1012827616	T -> DEL	N	N	silent_mutation	Average:7.489; most accessible tissue: Callus, score: 26.506	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1012827616	NA	5.87E-06	mr1328	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
vg1012827616	NA	6.87E-06	mr1169_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
vg1012827616	NA	7.73E-06	mr1236_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
vg1012827616	NA	7.53E-07	mr1446_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
vg1012827616	NA	1.66E-09	mr1567_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
vg1012827616	NA	1.45E-06	mr1567_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
vg1012827616	NA	1.87E-10	mr1806_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
vg1012827616	NA	3.20E-14	mr1846_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
vg1012827616	NA	8.92E-09	mr1909_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
vg1012827616	NA	9.77E-11	mr1921_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
vg1012827616	NA	2.84E-06	mr1951_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