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Detailed information for vg0901048761:

Variant ID: vg0901048761 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 1048761
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.95, G: 0.05, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

CGCGGGAGAGAGATATTTAGTCCCGAATATATGATACCAACCGGGACTAAATATATGATCTTTAGTCCCGAATGGTGTTACCAACCAGGACTAAAGATCA[A/G]
AAAGTACCGTTGGGCTTTTGAACCGGGATTAAAAATATTTTTTTAGTCCCGGTTACTATTCGAACTAGGACTAATGTGATTTTTGCCATCTGGATAAAGA

Reverse complement sequence

TCTTTATCCAGATGGCAAAAATCACATTAGTCCTAGTTCGAATAGTAACCGGGACTAAAAAAATATTTTTAATCCCGGTTCAAAAGCCCAACGGTACTTT[T/C]
TGATCTTTAGTCCTGGTTGGTAACACCATTCGGGACTAAAGATCATATATTTAGTCCCGGTTGGTATCATATATTCGGGACTAAATATCTCTCTCCCGCG

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	96.00%	4.00%	0.00%	0.00%	NA
All Indica	2759	98.10%	1.90%	0.00%	0.00%	NA
All Japonica	1512	93.80%	6.20%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	97.20%	2.80%	0.00%	0.00%	NA
Indica Intermediate	786	97.10%	2.90%	0.00%	0.00%	NA
Temperate Japonica	767	99.10%	0.90%	0.00%	0.00%	NA
Tropical Japonica	504	95.40%	4.60%	0.00%	0.00%	NA
Japonica Intermediate	241	73.40%	26.60%	0.00%	0.00%	NA
VI/Aromatic	96	61.50%	38.50%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0901048761	A -> G	LOC_Os09g02520.1	upstream_gene_variant ; 3690.0bp to feature; MODIFIER	silent_mutation	Average:70.055; most accessible tissue: Zhenshan97 young leaf, score: 84.035	N	N	N	N
vg0901048761	A -> G	LOC_Os09g02510.1	downstream_gene_variant ; 43.0bp to feature; MODIFIER	silent_mutation	Average:70.055; most accessible tissue: Zhenshan97 young leaf, score: 84.035	N	N	N	N
vg0901048761	A -> G	LOC_Os09g02500-LOC_Os09g02510	intergenic_region ; MODIFIER	silent_mutation	Average:70.055; most accessible tissue: Zhenshan97 young leaf, score: 84.035	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0901048761	4.02E-08	4.02E-08	mr1008	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
vg0901048761	1.79E-09	1.79E-09	mr1009	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
vg0901048761	4.58E-08	NA	mr1023	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
vg0901048761	1.17E-07	NA	mr1023	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
vg0901048761	3.85E-06	NA	mr1079	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
vg0901048761	3.68E-06	NA	mr1079	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
vg0901048761	3.84E-08	NA	mr1142	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
vg0901048761	2.06E-07	NA	mr1142	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
vg0901048761	NA	2.54E-07	mr1242	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
vg0901048761	NA	3.53E-06	mr1247	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
vg0901048761	1.22E-08	NA	mr1489	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
vg0901048761	8.93E-08	NA	mr1489	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
vg0901048761	8.34E-08	NA	mr1491	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
vg0901048761	1.09E-07	NA	mr1491	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
vg0901048761	6.00E-07	NA	mr1778	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
vg0901048761	1.14E-07	NA	mr1778	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
vg0901048761	NA	3.53E-06	mr1114_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
vg0901048761	NA	6.04E-07	mr1240_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