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Detailed information for vg0604304747:

Variant ID: vg0604304747 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 4304747
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

ACTAATTTGAATGAGAGGATCTTAGCAAATTATTGTCTTAACAAATTAATTCCCATATTAGCTCTTATGGTGCTAGCTGGTAATACCTCTGGTCTTTTTC[G/A]
AAAAGCTCGATATATATGAGAGGAGGAGCTCACATGTTGATGTTTACTAATGCTATTCTCGGTTCCGTGGGTTGGGAACTAACACTCCTGCACACGCAAA

Reverse complement sequence

TTTGCGTGTGCAGGAGTGTTAGTTCCCAACCCACGGAACCGAGAATAGCATTAGTAAACATCAACATGTGAGCTCCTCCTCTCATATATATCGAGCTTTT[C/T]
GAAAAAGACCAGAGGTATTACCAGCTAGCACCATAAGAGCTAATATGGGAATTAATTTGTTAAGACAATAATTTGCTAAGATCCTCTCATTCAAATTAGT

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	68.20%	31.40%	0.32%	0.00%	NA
All Indica	2759	86.30%	13.30%	0.43%	0.00%	NA
All Japonica	1512	40.70%	59.20%	0.07%	0.00%	NA
Aus	269	28.30%	71.40%	0.37%	0.00%	NA
Indica I	595	77.30%	21.70%	1.01%	0.00%	NA
Indica II	465	88.20%	11.60%	0.22%	0.00%	NA
Indica III	913	96.50%	3.50%	0.00%	0.00%	NA
Indica Intermediate	786	80.00%	19.30%	0.64%	0.00%	NA
Temperate Japonica	767	4.40%	95.60%	0.00%	0.00%	NA
Tropical Japonica	504	90.70%	9.30%	0.00%	0.00%	NA
Japonica Intermediate	241	51.90%	47.70%	0.41%	0.00%	NA
VI/Aromatic	96	81.20%	17.70%	1.04%	0.00%	NA
Intermediate	90	83.30%	16.70%	0.00%	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
vg0604304747	G -> A	LOC_Os06g08640.1	upstream_gene_variant ; 1626.0bp to feature; MODIFIER	silent_mutation	Average:35.563; most accessible tissue: Callus, score: 80.35	N	N	N	N
vg0604304747	G -> A	LOC_Os06g08640-LOC_Os06g08650	intergenic_region ; MODIFIER	silent_mutation	Average:35.563; most accessible tissue: Callus, score: 80.35	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0604304747	8.34E-06	NA	mr1115	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
vg0604304747	2.78E-09	8.30E-24	mr1115	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
vg0604304747	7.35E-09	NA	mr1241	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
vg0604304747	NA	1.02E-12	mr1241	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
vg0604304747	NA	5.50E-08	mr1552	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
vg0604304747	2.27E-08	1.28E-28	mr1611	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
vg0604304747	NA	3.59E-06	mr1611	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
vg0604304747	NA	9.16E-16	mr1611	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
vg0604304747	NA	8.13E-07	mr1772	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
vg0604304747	6.54E-10	4.39E-29	mr1920	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
vg0604304747	2.12E-06	9.64E-09	mr1920	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
vg0604304747	NA	1.33E-14	mr1920	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
vg0604304747	NA	2.59E-07	mr1090_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
vg0604304747	1.80E-09	2.03E-24	mr1115_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
vg0604304747	NA	3.98E-06	mr1211_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
vg0604304747	1.07E-09	NA	mr1241_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
vg0604304747	4.88E-08	6.24E-20	mr1241_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
vg0604304747	NA	2.76E-06	mr1363_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
vg0604304747	1.05E-06	9.78E-17	mr1611_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
vg0604304747	NA	3.75E-07	mr1629_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
vg0604304747	NA	9.07E-07	mr1793_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