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Detailed information for vg0709322762:

Variant ID: vg0709322762 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 9322762
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, G: 0.06, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

CAACGTTTGCTTTGCCGGGGTGGTAGTGAACCTCTAGATCATAGTCCTTGATTAATTCCAGCCATCGCCTTTGCCTCAAGTTGAGATCTGACTGGGTGAA[A/G]
ATATACTTCAGACTCTTGTGGTCAATGTAGATATCGCAATGGTTTCCAATCAAGTAGTGTCTCCAAATCTTTAGCGCATGAACCACGGCTGCTAGTTCTA

Reverse complement sequence

TAGAACTAGCAGCCGTGGTTCATGCGCTAAAGATTTGGAGACACTACTTGATTGGAAACCATTGCGATATCTACATTGACCACAAGAGTCTGAAGTATAT[T/C]
TTCACCCAGTCAGATCTCAACTTGAGGCAAAGGCGATGGCTGGAATTAATCAAGGACTATGATCTAGAGGTTCACTACCACCCCGGCAAAGCAAACGTTG

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	39.00%	0.20%	11.96%	48.86%	NA
All Indica	2759	5.20%	0.30%	17.25%	77.27%	NA
All Japonica	1512	94.30%	0.00%	1.92%	3.77%	NA
Aus	269	68.40%	0.40%	11.90%	19.33%	NA
Indica I	595	4.70%	1.00%	15.63%	78.66%	NA
Indica II	465	6.20%	0.00%	11.18%	82.58%	NA
Indica III	913	3.70%	0.00%	16.10%	80.18%	NA
Indica Intermediate	786	6.60%	0.30%	23.41%	69.72%	NA
Temperate Japonica	767	96.90%	0.00%	0.52%	2.61%	NA
Tropical Japonica	504	88.90%	0.00%	4.56%	6.55%	NA
Japonica Intermediate	241	97.50%	0.00%	0.83%	1.66%	NA
VI/Aromatic	96	51.00%	0.00%	25.00%	23.96%	NA
Intermediate	90	45.60%	0.00%	4.44%	50.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0709322762	A -> DEL	LOC_Os07g16000.1	N	frameshift_variant	Average:22.075; most accessible tissue: Callus, score: 34.995	N	N	N	N
vg0709322762	A -> G	LOC_Os07g16000.1	synonymous_variant ; p.Ile1130Ile; LOW	synonymous_codon	Average:22.075; most accessible tissue: Callus, score: 34.995	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0709322762	NA	3.19E-10	mr1316	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
vg0709322762	NA	3.91E-10	mr1524	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
vg0709322762	NA	5.82E-12	mr1657	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
vg0709322762	NA	7.19E-07	mr1717	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
vg0709322762	NA	1.50E-08	mr1827	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
vg0709322762	NA	5.50E-15	mr1916	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
vg0709322762	NA	2.85E-16	mr1260_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
vg0709322762	2.52E-06	NA	mr1296_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
vg0709322762	3.72E-06	NA	mr1296_2	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
vg0709322762	NA	2.01E-12	mr1728_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