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Detailed information for vg0812659623:

Variant ID: vg0812659623 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 12659623
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.03, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

TTATGCCCCATATGCCTTTGAGTAAGTTGTAATATATATGCACTAAGAGTATATACATATAATCATGGCTCGACTAACAATTTCGTTTGCAGCGACCATT[A/G]
GATAGTCTTTCTTCTCTATCCAAAGTACAATGAAGTCATCGTCTTGGATTCTCTCGACAAAGATAGCAACACCTATCAGGAATTTCTAAGAATTATCGAT

Reverse complement sequence

ATCGATAATTCTTAGAAATTCCTGATAGGTGTTGCTATCTTTGTCGAGAGAATCCAAGACGATGACTTCATTGTACTTTGGATAGAGAAGAAAGACTATC[T/C]
AATGGTCGCTGCAAACGAAATTGTTAGTCGAGCCATGATTATATGTATATACTCTTAGTGCATATATATTACAACTTACTCAAAGGCATATGGGGCATAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	40.00%	0.80%	6.12%	53.07%	NA
All Indica	2759	23.70%	1.10%	8.34%	66.91%	NA
All Japonica	1512	67.50%	0.00%	0.86%	31.68%	NA
Aus	269	59.50%	1.90%	8.55%	30.11%	NA
Indica I	595	12.10%	0.30%	4.20%	83.36%	NA
Indica II	465	19.80%	2.40%	6.67%	71.18%	NA
Indica III	913	32.10%	0.30%	10.30%	57.28%	NA
Indica Intermediate	786	24.90%	1.80%	10.18%	63.10%	NA
Temperate Japonica	767	90.10%	0.00%	0.13%	9.78%	NA
Tropical Japonica	504	42.70%	0.00%	1.98%	55.36%	NA
Japonica Intermediate	241	47.30%	0.00%	0.83%	51.87%	NA
VI/Aromatic	96	14.60%	4.20%	19.79%	61.46%	NA
Intermediate	90	47.80%	0.00%	4.44%	47.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0812659623	A -> G	LOC_Os08g21190.1	upstream_gene_variant ; 4650.0bp to feature; MODIFIER	silent_mutation	Average:8.33; most accessible tissue: Minghui63 root, score: 13.235	N	N	N	N
vg0812659623	A -> G	LOC_Os08g21210.1	downstream_gene_variant ; 1894.0bp to feature; MODIFIER	silent_mutation	Average:8.33; most accessible tissue: Minghui63 root, score: 13.235	N	N	N	N
vg0812659623	A -> G	LOC_Os08g21200.1	intron_variant ; MODIFIER	silent_mutation	Average:8.33; most accessible tissue: Minghui63 root, score: 13.235	N	N	N	N
vg0812659623	A -> DEL	N	N	silent_mutation	Average:8.33; most accessible tissue: Minghui63 root, score: 13.235	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0812659623	NA	1.46E-08	mr1045	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
vg0812659623	NA	3.13E-07	mr1129	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
vg0812659623	NA	7.84E-06	mr1257	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
vg0812659623	NA	7.31E-06	mr1309	Ind_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
vg0812659623	5.73E-06	2.28E-06	mr1400	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
vg0812659623	NA	5.00E-06	mr1483	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
vg0812659623	NA	3.15E-08	mr1599	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
vg0812659623	NA	1.58E-06	mr1704	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
vg0812659623	NA	6.60E-06	mr1708	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
vg0812659623	NA	7.86E-13	mr1746	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
vg0812659623	NA	9.97E-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
vg0812659623	NA	3.11E-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
vg0812659623	NA	1.32E-07	mr1785	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
vg0812659623	NA	5.77E-06	mr1844	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
vg0812659623	2.32E-06	NA	mr1883	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
vg0812659623	1.86E-07	1.86E-07	mr1883	Ind_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