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Detailed information for vg0907965825:

Variant ID: vg0907965825 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7965825
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

TATATGCAACTAATCCTTTAATTAATTAAAAACGAAGAGTACAGGCGGATTTCCTTTGATGCTCACACGTGAGATATATACATATAACTACAAAAAGAAT[A/G]
TCTAAACGATTCTTAATTTCCTCTCTGAACGATGCTTGAAATTTTGTCTCAAAACATTAAAAAAATAATTTACCTAAAAAATGGTAAAATTTTGTAGTTC

Reverse complement sequence

GAACTACAAAATTTTACCATTTTTTAGGTAAATTATTTTTTTAATGTTTTGAGACAAAATTTCAAGCATCGTTCAGAGAGGAAATTAAGAATCGTTTAGA[T/C]
ATTCTTTTTGTAGTTATATGTATATATCTCACGTGTGAGCATCAAAGGAAATCCGCCTGTACTCTTCGTTTTTAATTAATTAAAGGATTAGTTGCATATA

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	79.80%	20.10%	0.17%	0.00%	NA
All Indica	2759	94.20%	5.70%	0.11%	0.00%	NA
All Japonica	1512	48.40%	51.30%	0.26%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	95.60%	4.20%	0.17%	0.00%	NA
Indica II	465	88.80%	10.80%	0.43%	0.00%	NA
Indica III	913	99.10%	0.90%	0.00%	0.00%	NA
Indica Intermediate	786	90.70%	9.30%	0.00%	0.00%	NA
Temperate Japonica	767	36.40%	63.20%	0.39%	0.00%	NA
Tropical Japonica	504	76.80%	23.00%	0.20%	0.00%	NA
Japonica Intermediate	241	27.40%	72.60%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	81.10%	17.80%	1.11%	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
vg0907965825	A -> G	LOC_Os09g13650.1	intron_variant ; MODIFIER	silent_mutation	Average:30.97; most accessible tissue: Callus, score: 58.369	N	N	N	N
vg0907965825	A -> G	LOC_Os09g13650.2	intron_variant ; MODIFIER	silent_mutation	Average:30.97; most accessible tissue: Callus, score: 58.369	N	N	N	N
vg0907965825	A -> G	LOC_Os09g13650.3	intron_variant ; MODIFIER	silent_mutation	Average:30.97; most accessible tissue: Callus, score: 58.369	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907965825	2.26E-06	6.62E-13	mr1002	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
vg0907965825	6.62E-06	1.05E-13	mr1002	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
vg0907965825	NA	9.20E-10	mr1282	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
vg0907965825	NA	3.28E-09	mr1658	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
vg0907965825	NA	3.22E-14	mr1002_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
vg0907965825	NA	7.45E-11	mr1002_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
vg0907965825	NA	2.87E-07	mr1030_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
vg0907965825	NA	6.08E-06	mr1330_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
vg0907965825	NA	2.34E-06	mr1379_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
vg0907965825	NA	1.21E-06	mr1555_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
vg0907965825	NA	2.55E-08	mr1709_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
vg0907965825	NA	4.09E-07	mr1748_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
vg0907965825	NA	4.11E-10	mr1805_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