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Detailed information for vg0123559107:

Variant ID: vg0123559107 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 23559107
Reference Allele: A	Alternative Allele: G
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: 96. )

Flanking Sequence (100 bp) in Reference Genome:

CATAATTAGAAAAAGTTTATTGTAACATCACATTGTCAAAATCATGACGTAATTAGACTTAAAAGATTCGTCTCGCGAATTAGTCCAAGGATATGGAATG[A/G]
GTTTTGTAATTAGTGTATGTTTAATACTCTAAATTAGTGTCCAAACATCCAATATGACAGGGACTCACTGGAAACCAAACAGGCCCTAAGTATGCGAAGA

Reverse complement sequence

TCTTCGCATACTTAGGGCCTGTTTGGTTTCCAGTGAGTCCCTGTCATATTGGATGTTTGGACACTAATTTAGAGTATTAAACATACACTAATTACAAAAC[T/C]
CATTCCATATCCTTGGACTAATTCGCGAGACGAATCTTTTAAGTCTAATTACGTCATGATTTTGACAATGTGATGTTACAATAAACTTTTTCTAATTATG

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	82.20%	9.40%	0.32%	8.08%	NA
All Indica	2759	95.00%	0.50%	0.00%	4.49%	NA
All Japonica	1512	72.00%	27.10%	0.53%	0.33%	NA
Aus	269	8.20%	1.10%	2.60%	88.10%	NA
Indica I	595	99.80%	0.00%	0.00%	0.17%	NA
Indica II	465	98.70%	0.40%	0.00%	0.86%	NA
Indica III	913	91.30%	0.30%	0.00%	8.32%	NA
Indica Intermediate	786	93.30%	1.30%	0.00%	5.47%	NA
Temperate Japonica	767	55.70%	43.40%	0.91%	0.00%	NA
Tropical Japonica	504	97.80%	2.20%	0.00%	0.00%	NA
Japonica Intermediate	241	70.10%	27.40%	0.41%	2.07%	NA
VI/Aromatic	96	89.60%	1.00%	0.00%	9.38%	NA
Intermediate	90	76.70%	15.60%	0.00%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0123559107	A -> G	LOC_Os01g41610.1	upstream_gene_variant ; 1453.0bp to feature; MODIFIER	silent_mutation	Average:25.621; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg0123559107	A -> G	LOC_Os01g41610.2	upstream_gene_variant ; 1453.0bp to feature; MODIFIER	silent_mutation	Average:25.621; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg0123559107	A -> G	LOC_Os01g41600.1	downstream_gene_variant ; 4855.0bp to feature; MODIFIER	silent_mutation	Average:25.621; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg0123559107	A -> G	LOC_Os01g41620.1	downstream_gene_variant ; 2598.0bp to feature; MODIFIER	silent_mutation	Average:25.621; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg0123559107	A -> G	LOC_Os01g41610-LOC_Os01g41620	intergenic_region ; MODIFIER	silent_mutation	Average:25.621; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg0123559107	A -> DEL	N	N	silent_mutation	Average:25.621; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0123559107	NA	5.90E-08	mr1531_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
vg0123559107	2.60E-06	NA	mr1970_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