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Detailed information for vg0801363085:

Variant ID: vg0801363085 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 1363085
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGAAGGCACACTAGTGAGGGCAAAGGCCTTAGGCTAACAAAAAAACAAAATTTATTTTTTTTTGAATTATACTCATCTGTGACGGGCTATAATCTAGAC[C/T]
CGTTAGAGATGAGAGTCATCCGTGACGGGCTATAATCTAGGCCCGTTAGAGATGAGAGTCATCCATGACGGGCTTTTATGTTGGCTTGATTGAGATGTGT

Reverse complement sequence

ACACATCTCAATCAAGCCAACATAAAAGCCCGTCATGGATGACTCTCATCTCTAACGGGCCTAGATTATAGCCCGTCACGGATGACTCTCATCTCTAACG[G/A]
GTCTAGATTATAGCCCGTCACAGATGAGTATAATTCAAAAAAAAATAAATTTTGTTTTTTTGTTAGCCTAAGGCCTTTGCCCTCACTAGTGTGCCTTCCT

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	74.20%	0.40%	3.41%	21.98%	NA
All Indica	2759	64.10%	0.30%	3.12%	32.51%	NA
All Japonica	1512	98.80%	0.00%	0.07%	1.12%	NA
Aus	269	33.80%	3.70%	26.39%	36.06%	NA
Indica I	595	55.30%	0.30%	3.87%	40.50%	NA
Indica II	465	58.70%	0.00%	2.15%	39.14%	NA
Indica III	913	75.80%	0.30%	1.64%	22.23%	NA
Indica Intermediate	786	60.30%	0.40%	4.83%	34.48%	NA
Temperate Japonica	767	98.60%	0.00%	0.13%	1.30%	NA
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	98.30%	0.00%	0.00%	1.66%	NA
VI/Aromatic	96	86.50%	0.00%	1.04%	12.50%	NA
Intermediate	90	80.00%	0.00%	2.22%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0801363085	C -> T	LOC_Os08g03050.1	upstream_gene_variant ; 4632.0bp to feature; MODIFIER	silent_mutation	Average:13.774; most accessible tissue: Callus, score: 43.743	N	N	N	N
vg0801363085	C -> T	LOC_Os08g03040.1	downstream_gene_variant ; 1887.0bp to feature; MODIFIER	silent_mutation	Average:13.774; most accessible tissue: Callus, score: 43.743	N	N	N	N
vg0801363085	C -> T	LOC_Os08g03030-LOC_Os08g03040	intergenic_region ; MODIFIER	silent_mutation	Average:13.774; most accessible tissue: Callus, score: 43.743	N	N	N	N
vg0801363085	C -> DEL	N	N	silent_mutation	Average:13.774; most accessible tissue: Callus, score: 43.743	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0801363085	7.59E-07	NA	mr1593	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