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Detailed information for vg0805694237:

Variant ID: vg0805694237 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 5694237
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCAACTGGGCCTTGAATCTGTTTCTTCCAGCTATATGTAAGCATATCACACCCCTCTGGTTTTGTCAATACACTCTTGCCTATTTTTTTCTGTATCTCA[A/T]
CCTCTTTTGTGATCTTGCATACAGATGCAGCCGTACAGGTACAGGAATGTGGTTGAGCAGTTCGTCAGAAGAGCCGAGAGAGCTGGGTTCAAGGCGATTG

Reverse complement sequence

CAATCGCCTTGAACCCAGCTCTCTCGGCTCTTCTGACGAACTGCTCAACCACATTCCTGTACCTGTACGGCTGCATCTGTATGCAAGATCACAAAAGAGG[T/A]
TGAGATACAGAAAAAAATAGGCAAGAGTGTATTGACAAAACCAGAGGGGTGTGATATGCTTACATATAGCTGGAAGAAACAGATTCAAGGCCCAGTTGAG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.60%	23.00%	2.37%	21.03%	NA
All Indica	2759	70.50%	1.10%	1.38%	27.04%	NA
All Japonica	1512	27.10%	68.30%	4.23%	0.46%	NA
Aus	269	21.20%	0.40%	1.12%	77.32%	NA
Indica I	595	55.00%	0.30%	1.34%	43.36%	NA
Indica II	465	87.50%	3.00%	2.37%	7.10%	NA
Indica III	913	71.60%	0.40%	0.66%	27.27%	NA
Indica Intermediate	786	70.90%	1.30%	1.65%	26.21%	NA
Temperate Japonica	767	32.70%	60.10%	6.91%	0.26%	NA
Tropical Japonica	504	18.10%	81.00%	0.20%	0.79%	NA
Japonica Intermediate	241	27.80%	67.60%	4.15%	0.41%	NA
VI/Aromatic	96	75.00%	0.00%	1.04%	23.96%	NA
Intermediate	90	54.40%	27.80%	6.67%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0805694237	A -> T	LOC_Os08g09850.1	upstream_gene_variant ; 4893.0bp to feature; MODIFIER	silent_mutation	Average:41.376; most accessible tissue: Callus, score: 74.774	N	N	N	N
vg0805694237	A -> T	LOC_Os08g09870.1	downstream_gene_variant ; 2419.0bp to feature; MODIFIER	silent_mutation	Average:41.376; most accessible tissue: Callus, score: 74.774	N	N	N	N
vg0805694237	A -> T	LOC_Os08g09860.1	intron_variant ; MODIFIER	silent_mutation	Average:41.376; most accessible tissue: Callus, score: 74.774	N	N	N	N
vg0805694237	A -> DEL	N	N	silent_mutation	Average:41.376; most accessible tissue: Callus, score: 74.774	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0805694237	NA	9.43E-13	mr1579	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
vg0805694237	NA	1.34E-12	mr1636	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
vg0805694237	NA	2.00E-10	mr1921	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
vg0805694237	NA	3.37E-07	mr1020_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
vg0805694237	NA	2.19E-07	mr1205_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
vg0805694237	NA	2.26E-09	mr1232_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
vg0805694237	1.20E-06	NA	mr1482_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
vg0805694237	NA	4.03E-08	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