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Detailed information for vg0419763973:

Variant ID: vg0419763973 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 19763973
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCGTCACCCTCTCTCCTCTCCGCCCGCGCGCGCGCTTTGGGCCGCCTTCTTGGGCCGGCCGGCCCATTTAGCTCGGCCGAGCCGCCCCTTCCTCTCGAG[C/T]
CGCGCCCTAGCCGCCCGAGGGAAGTCTGATTTCCCTCCCTCCTTCTTTTCTTTTCTTTTTCTTTTTCAAAAAGGATTTAAATAAATCCTTTTTCCTTTAG

Reverse complement sequence

CTAAAGGAAAAAGGATTTATTTAAATCCTTTTTGAAAAAGAAAAAGAAAAGAAAAGAAGGAGGGAGGGAAATCAGACTTCCCTCGGGCGGCTAGGGCGCG[G/A]
CTCGAGAGGAAGGGGCGGCTCGGCCGAGCTAAATGGGCCGGCCGGCCCAAGAAGGCGGCCCAAAGCGCGCGCGCGGGCGGAGAGGAGAGAGGGTGACGGT

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	71.00%	3.60%	13.71%	11.66%	NA
All Indica	2759	56.80%	6.00%	21.38%	15.80%	NA
All Japonica	1512	94.80%	0.00%	0.73%	4.50%	NA
Aus	269	70.60%	1.50%	14.87%	13.01%	NA
Indica I	595	40.30%	4.00%	35.13%	20.50%	NA
Indica II	465	61.90%	2.40%	16.77%	18.92%	NA
Indica III	913	65.70%	9.60%	15.12%	9.53%	NA
Indica Intermediate	786	55.90%	5.50%	20.99%	17.68%	NA
Temperate Japonica	767	90.20%	0.00%	1.17%	8.60%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	98.80%	0.00%	0.83%	0.41%	NA
VI/Aromatic	96	96.90%	0.00%	3.12%	0.00%	NA
Intermediate	90	82.20%	0.00%	4.44%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0419763973	C -> DEL	N	N	silent_mutation	Average:17.741; most accessible tissue: Callus, score: 36.897	N	N	N	N
vg0419763973	C -> T	LOC_Os04g32770.1	upstream_gene_variant ; 2053.0bp to feature; MODIFIER	silent_mutation	Average:17.741; most accessible tissue: Callus, score: 36.897	N	N	N	N
vg0419763973	C -> T	LOC_Os04g32760.1	downstream_gene_variant ; 1965.0bp to feature; MODIFIER	silent_mutation	Average:17.741; most accessible tissue: Callus, score: 36.897	N	N	N	N
vg0419763973	C -> T	LOC_Os04g32760-LOC_Os04g32770	intergenic_region ; MODIFIER	silent_mutation	Average:17.741; most accessible tissue: Callus, score: 36.897	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0419763973	2.82E-06	NA	mr1457	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