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Detailed information for vg0808077570:

Variant ID: vg0808077570 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8077570
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.09, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:

GATTTTGAAGAAGATGCACTCATAGTAGACATGATACCAGTAGATTTAAACACAGTTTTGTTAGTATCAGGTTTAACCAAAATCTCACCACTTCTAGCAC[T/C]
AACACCTAACACAACAGGAGGATGTCTAGAATTATGAGCATAAGGATTAAAACCTAAACCACGGTTATGTGTGCTAACCTTTGATTGATCCAAAATCATG

Reverse complement sequence

CATGATTTTGGATCAATCAAAGGTTAGCACACATAACCGTGGTTTAGGTTTTAATCCTTATGCTCATAATTCTAGACATCCTCCTGTTGTGTTAGGTGTT[A/G]
GTGCTAGAAGTGGTGAGATTTTGGTTAAACCTGATACTAACAAAACTGTGTTTAAATCTACTGGTATCATGTCTACTATGAGTGCATCTTCTTCAAAATC

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	63.30%	34.40%	0.55%	1.69%	NA
All Indica	2759	90.40%	5.90%	0.72%	2.90%	NA
All Japonica	1512	10.30%	89.40%	0.26%	0.00%	NA
Aus	269	95.90%	3.70%	0.37%	0.00%	NA
Indica I	595	87.70%	9.70%	0.84%	1.68%	NA
Indica II	465	94.40%	4.70%	0.65%	0.22%	NA
Indica III	913	91.90%	2.60%	0.44%	5.04%	NA
Indica Intermediate	786	88.40%	7.60%	1.02%	2.93%	NA
Temperate Japonica	767	2.90%	97.00%	0.13%	0.00%	NA
Tropical Japonica	504	20.80%	79.00%	0.20%	0.00%	NA
Japonica Intermediate	241	12.00%	87.10%	0.83%	0.00%	NA
VI/Aromatic	96	29.20%	70.80%	0.00%	0.00%	NA
Intermediate	90	62.20%	36.70%	1.11%	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
vg0808077570	T -> C	LOC_Os08g13600.1	upstream_gene_variant ; 2773.0bp to feature; MODIFIER	silent_mutation	Average:23.253; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0808077570	T -> C	LOC_Os08g13590.1	intron_variant ; MODIFIER	silent_mutation	Average:23.253; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0808077570	T -> DEL	N	N	silent_mutation	Average:23.253; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808077570	NA	8.17E-06	mr1209	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
vg0808077570	NA	4.13E-15	mr1376	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
vg0808077570	NA	4.13E-15	mr1431	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
vg0808077570	NA	7.61E-14	mr1653	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
vg0808077570	NA	3.02E-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
vg0808077570	2.51E-06	5.45E-07	mr1098_2	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
vg0808077570	5.30E-06	1.34E-06	mr1114_2	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
vg0808077570	9.39E-06	NA	mr1123_2	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
vg0808077570	5.11E-06	1.02E-06	mr1150_2	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
vg0808077570	1.37E-06	9.86E-07	mr1242_2	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