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Detailed information for vg1019751150:

Variant ID: vg1019751150 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 19751150
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

AATCAGTACGAACATACATACAAAAGTTTTACTCGCATATCATTTTTTAATCGCTAATAAGCCATTATAGCTTATAACAAGTATTACCAACCGATGGGGA[C/T]
TTGATATTTTACTTGCACTGTTTGATCACTCGTCTTATTTAAAAAATTTGTGTAAATATAAAAAATGAAAAATTATGCTTAAAGTACTTTGGATAATAAA

Reverse complement sequence

TTTATTATCCAAAGTACTTTAAGCATAATTTTTCATTTTTTATATTTACACAAATTTTTTAAATAAGACGAGTGATCAAACAGTGCAAGTAAAATATCAA[G/A]
TCCCCATCGGTTGGTAATACTTGTTATAAGCTATAATGGCTTATTAGCGATTAAAAAATGATATGCGAGTAAAACTTTTGTATGTATGTTCGTACTGATT

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	54.40%	43.10%	2.45%	0.00%	NA
All Indica	2759	24.70%	71.60%	3.66%	0.00%	NA
All Japonica	1512	97.60%	1.70%	0.73%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	5.50%	86.90%	7.56%	0.00%	NA
Indica II	465	31.40%	66.00%	2.58%	0.00%	NA
Indica III	913	26.40%	72.80%	0.77%	0.00%	NA
Indica Intermediate	786	33.30%	62.00%	4.71%	0.00%	NA
Temperate Japonica	767	98.80%	0.90%	0.26%	0.00%	NA
Tropical Japonica	504	95.20%	3.20%	1.59%	0.00%	NA
Japonica Intermediate	241	98.80%	0.80%	0.41%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	57.80%	37.80%	4.44%	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
vg1019751150	C -> T	LOC_Os10g36860.1	upstream_gene_variant ; 1524.0bp to feature; MODIFIER	silent_mutation	Average:24.351; most accessible tissue: Callus, score: 49.074	N	N	N	N
vg1019751150	C -> T	LOC_Os10g36870.1	downstream_gene_variant ; 330.0bp to feature; MODIFIER	silent_mutation	Average:24.351; most accessible tissue: Callus, score: 49.074	N	N	N	N
vg1019751150	C -> T	LOC_Os10g36860-LOC_Os10g36870	intergenic_region ; MODIFIER	silent_mutation	Average:24.351; most accessible tissue: Callus, score: 49.074	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1019751150	9.74E-07	NA	mr1354_2	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