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Detailed information for vg0432785736:

Variant ID: vg0432785736 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32785736
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTATATATAGGGGATAAAAGAAAGACACCTAATAGGACTTCTACTAGGAAACTAATCCGATAATATTGTGGGCCCAAAATTCGGATCACATATTTAACA[C/T]
AAAGGGTGTAATTTATCTATTTGGAGCAAAGGAAGAAGAACAAATCTTCGTATATAAGAGCTAAAAGTGTGGAATTGTATAACTTATTATCGACTATGAG

Reverse complement sequence

CTCATAGTCGATAATAAGTTATACAATTCCACACTTTTAGCTCTTATATACGAAGATTTGTTCTTCTTCCTTTGCTCCAAATAGATAAATTACACCCTTT[G/A]
TGTTAAATATGTGATCCGAATTTTGGGCCCACAATATTATCGGATTAGTTTCCTAGTAGAAGTCCTATTAGGTGTCTTTCTTTTATCCCCTATATATACT

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	95.80%	4.20%	0.00%	0.00%	NA
All Indica	2759	98.20%	1.80%	0.00%	0.00%	NA
All Japonica	1512	90.50%	9.50%	0.00%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	96.70%	3.30%	0.00%	0.00%	NA
Indica Intermediate	786	97.70%	2.30%	0.00%	0.00%	NA
Temperate Japonica	767	98.70%	1.30%	0.00%	0.00%	NA
Tropical Japonica	504	76.00%	24.00%	0.00%	0.00%	NA
Japonica Intermediate	241	94.60%	5.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0432785736	C -> T	LOC_Os04g55140.1	upstream_gene_variant ; 740.0bp to feature; MODIFIER	silent_mutation	Average:49.679; most accessible tissue: Callus, score: 77.087	N	N	N	N
vg0432785736	C -> T	LOC_Os04g55150.2	upstream_gene_variant ; 2980.0bp to feature; MODIFIER	silent_mutation	Average:49.679; most accessible tissue: Callus, score: 77.087	N	N	N	N
vg0432785736	C -> T	LOC_Os04g55140-LOC_Os04g55150	intergenic_region ; MODIFIER	silent_mutation	Average:49.679; most accessible tissue: Callus, score: 77.087	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432785736	NA	3.84E-07	mr1206	Jap_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
vg0432785736	4.50E-07	4.50E-07	mr1663	Jap_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
vg0432785736	NA	9.29E-09	mr1746	Jap_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