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Detailed information for vg0823822394:

Variant ID: vg0823822394 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 23822394
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

TAATGGATCTTTCCTTGTGCAAAAGTCAGCAATGCAGAAGAAGAATATGCTATTTATTTTACAAAAAAAGAAAAGAAAATTTTCAATCATGTTGAACATT[T/C]
TACCAACAGAAAGTGAAACATCTCCATAATCATGATTCATAATTTGAAAACCTGGGTTGATTCCGGATTGACAAAAACGTGTTCAGAGGAAAATGCTAAA

Reverse complement sequence

TTTAGCATTTTCCTCTGAACACGTTTTTGTCAATCCGGAATCAACCCAGGTTTTCAAATTATGAATCATGATTATGGAGATGTTTCACTTTCTGTTGGTA[A/G]
AATGTTCAACATGATTGAAAATTTTCTTTTCTTTTTTTGTAAAATAAATAGCATATTCTTCTTCTGCATTGCTGACTTTTGCACAAGGAAAGATCCATTA

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	84.70%	9.10%	6.22%	0.00%	NA
All Indica	2759	93.30%	1.40%	5.22%	0.00%	NA
All Japonica	1512	66.00%	25.30%	8.73%	0.00%	NA
Aus	269	95.90%	0.70%	3.35%	0.00%	NA
Indica I	595	84.00%	3.40%	12.61%	0.00%	NA
Indica II	465	95.10%	2.20%	2.80%	0.00%	NA
Indica III	913	99.30%	0.00%	0.66%	0.00%	NA
Indica Intermediate	786	92.40%	1.30%	6.36%	0.00%	NA
Temperate Japonica	767	44.50%	42.50%	13.04%	0.00%	NA
Tropical Japonica	504	94.60%	2.20%	3.17%	0.00%	NA
Japonica Intermediate	241	74.70%	18.70%	6.64%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	83.30%	7.80%	8.89%	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
vg0823822394	T -> C	LOC_Os08g37595.1	downstream_gene_variant ; 2422.0bp to feature; MODIFIER	silent_mutation	Average:43.374; most accessible tissue: Callus, score: 64.059	N	N	N	N
vg0823822394	T -> C	LOC_Os08g37600.1	intron_variant ; MODIFIER	silent_mutation	Average:43.374; most accessible tissue: Callus, score: 64.059	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0823822394	NA	2.59E-09	mr1137	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
vg0823822394	NA	1.68E-07	mr1202	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
vg0823822394	NA	4.72E-07	mr1229	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
vg0823822394	NA	3.62E-07	mr1252	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
vg0823822394	NA	5.17E-07	mr1271	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
vg0823822394	NA	6.21E-07	mr1596	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
vg0823822394	NA	3.51E-06	mr1596	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
vg0823822394	NA	6.42E-08	mr1617	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
vg0823822394	NA	6.04E-08	mr1748	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
vg0823822394	NA	6.04E-07	mr1763	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
vg0823822394	1.96E-06	NA	mr1768	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
vg0823822394	NA	5.30E-09	mr1880	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
vg0823822394	1.50E-06	7.09E-08	mr1955	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