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Detailed information for vg1008739198:

Variant ID: vg1008739198 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 8739198
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.71, A: 0.29, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TAGCCGCATTGAAGGGAGAAGCACCACCGCAGAAGGCCAGGATTCGTCTTACCGCAAGGAAGAGAGCTCTATTTGTCCCTCGCTACCAATTGGCGCCAAA[A/G]
GTCCGTGTGGTGGAGAAAGAAGTTACCCCAGCCCTAGCGGATCCTCCGGTCATCAACATAAGTGATGATTAAGAAGAAGAATCCAAGCACACTCATTCCA

Reverse complement sequence

TGGAATGAGTGTGCTTGGATTCTTCTTCTTAATCATCACTTATGTTGATGACCGGAGGATCCGCTAGGGCTGGGGTAACTTCTTTCTCCACCACACGGAC[T/C]
TTTGGCGCCAATTGGTAGCGAGGGACAAATAGAGCTCTCTTCCTTGCGGTAAGACGAATCCTGGCCTTCTGCGGTGGTGCTTCTCCCTTCAATGCGGCTA

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	31.70%	0.30%	42.98%	24.99%	NA
All Indica	2759	28.20%	0.30%	56.58%	14.93%	NA
All Japonica	1512	43.50%	0.30%	9.72%	46.49%	NA
Aus	269	2.20%	0.00%	88.85%	8.92%	NA
Indica I	595	15.10%	0.00%	56.81%	28.07%	NA
Indica II	465	23.40%	0.00%	61.08%	15.48%	NA
Indica III	913	44.10%	0.70%	50.05%	5.15%	NA
Indica Intermediate	786	22.50%	0.10%	61.32%	16.03%	NA
Temperate Japonica	767	58.40%	0.00%	3.26%	38.33%	NA
Tropical Japonica	504	14.30%	1.00%	22.02%	62.70%	NA
Japonica Intermediate	241	56.80%	0.00%	4.56%	38.59%	NA
VI/Aromatic	96	24.00%	2.10%	48.96%	25.00%	NA
Intermediate	90	37.80%	1.10%	41.11%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1008739198	A -> G	LOC_Os10g17350.1	synonymous_variant ; p.Lys227Lys; LOW	synonymous_codon	Average:10.672; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg1008739198	A -> DEL	LOC_Os10g17350.1	N	frameshift_variant	Average:10.672; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1008739198	NA	2.14E-07	mr1047	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
vg1008739198	NA	4.36E-06	mr1118	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
vg1008739198	NA	2.64E-06	mr1625	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
vg1008739198	NA	8.21E-06	mr1725	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
vg1008739198	NA	4.77E-06	mr1768	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
vg1008739198	9.07E-07	9.07E-07	mr1782	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
vg1008739198	NA	2.30E-06	mr1990	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
vg1008739198	NA	4.69E-06	mr1118_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
vg1008739198	NA	5.19E-07	mr1495_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
vg1008739198	NA	3.51E-06	mr1768_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