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Detailed information for vg1003124968:

Variant ID: vg1003124968 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3124968
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

ATATTTTGAACAACTTTTATATAGAAAATTTTCACACGAAACGCACTGTTTAGCAGTTTGAAAAGCATGCCACAAAAATCCAAAACTTTATCTCCCATGT[G/A]
TTGGGTTCTTAAACATGACCTTAGTAACTCCCTCCGTCCCAAAATATAACAACTTCGAGCCTCCAGATCTTTATCCCAAAATATAACAACTTCTACACCA

Reverse complement sequence

TGGTGTAGAAGTTGTTATATTTTGGGATAAAGATCTGGAGGCTCGAAGTTGTTATATTTTGGGACGGAGGGAGTTACTAAGGTCATGTTTAAGAACCCAA[C/T]
ACATGGGAGATAAAGTTTTGGATTTTTGTGGCATGCTTTTCAAACTGCTAAACAGTGCGTTTCGTGTGAAAATTTTCTATATAAAAGTTGTTCAAAATAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.80%	22.40%	0.83%	0.00%	NA
All Indica	2759	62.30%	37.30%	0.36%	0.00%	NA
All Japonica	1512	97.50%	0.90%	1.65%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	55.00%	44.50%	0.50%	0.00%	NA
Indica II	465	74.60%	24.70%	0.65%	0.00%	NA
Indica III	913	54.10%	45.70%	0.22%	0.00%	NA
Indica Intermediate	786	70.10%	29.60%	0.25%	0.00%	NA
Temperate Japonica	767	95.80%	1.30%	2.87%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	0.80%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	80.00%	15.60%	4.44%	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
vg1003124968	G -> A	LOC_Os10g06140.1	intron_variant ; MODIFIER	silent_mutation	Average:32.286; most accessible tissue: Callus, score: 56.213	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003124968	1.50E-13	NA	mr1538	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
vg1003124968	3.59E-12	1.12E-13	mr1538	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
vg1003124968	1.77E-21	4.07E-25	mr1547	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
vg1003124968	7.39E-17	1.42E-22	mr1547	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
vg1003124968	3.73E-44	1.13E-55	mr1709	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
vg1003124968	7.14E-43	1.05E-67	mr1709	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
vg1003124968	4.44E-12	NA	mr1538_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
vg1003124968	6.56E-15	4.48E-21	mr1538_2	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
vg1003124968	1.23E-18	1.30E-24	mr1547_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
vg1003124968	1.13E-20	6.39E-29	mr1547_2	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
vg1003124968	1.91E-60	1.74E-92	mr1709_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
vg1003124968	8.26E-64	2.46E-108	mr1709_2	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