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Detailed information for vg0124627219:

Variant ID: vg0124627219 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 24627219
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGTGGATAAAAATGTACATGCCAACTTGTCACAGAGATCTTGGGGTGCTTGATTTAGGGTATGTTTAGGTCCTTAGTAAAATTTTTCACCATGTCATAT[T/C]
GAATGTTTGGACACATATATGGAGTATTGAATATAAATGAAAAAAATAATTAATTACACAGATTGCGTGTAAATTGCGAGACGAATCTTTTAAGCTTAAT

Reverse complement sequence

ATTAAGCTTAAAAGATTCGTCTCGCAATTTACACGCAATCTGTGTAATTAATTATTTTTTTCATTTATATTCAATACTCCATATATGTGTCCAAACATTC[A/G]
ATATGACATGGTGAAAAATTTTACTAAGGACCTAAACATACCCTAAATCAAGCACCCCAAGATCTCTGTGACAAGTTGGCATGTACATTTTTATCCACTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.60%	34.30%	0.13%	0.00%	NA
All Indica	2759	96.70%	3.20%	0.07%	0.00%	NA
All Japonica	1512	19.00%	80.80%	0.20%	0.00%	NA
Aus	269	28.30%	71.70%	0.00%	0.00%	NA
Indica I	595	99.70%	0.20%	0.17%	0.00%	NA
Indica II	465	97.80%	2.20%	0.00%	0.00%	NA
Indica III	913	95.40%	4.60%	0.00%	0.00%	NA
Indica Intermediate	786	95.30%	4.60%	0.13%	0.00%	NA
Temperate Japonica	767	3.50%	96.50%	0.00%	0.00%	NA
Tropical Japonica	504	42.10%	57.50%	0.40%	0.00%	NA
Japonica Intermediate	241	19.90%	79.70%	0.41%	0.00%	NA
VI/Aromatic	96	17.70%	82.30%	0.00%	0.00%	NA
Intermediate	90	58.90%	40.00%	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
vg0124627219	T -> C	LOC_Os01g43150.1	upstream_gene_variant ; 4034.0bp to feature; MODIFIER	silent_mutation	Average:64.968; most accessible tissue: Zhenshan97 panicle, score: 87.126	N	N	N	N
vg0124627219	T -> C	LOC_Os01g43160.1	upstream_gene_variant ; 2051.0bp to feature; MODIFIER	silent_mutation	Average:64.968; most accessible tissue: Zhenshan97 panicle, score: 87.126	N	N	N	N
vg0124627219	T -> C	LOC_Os01g43150.3	upstream_gene_variant ; 4472.0bp to feature; MODIFIER	silent_mutation	Average:64.968; most accessible tissue: Zhenshan97 panicle, score: 87.126	N	N	N	N
vg0124627219	T -> C	LOC_Os01g43150-LOC_Os01g43160	intergenic_region ; MODIFIER	silent_mutation	Average:64.968; most accessible tissue: Zhenshan97 panicle, score: 87.126	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0124627219	NA	9.71E-08	mr1045	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
vg0124627219	NA	5.40E-10	mr1746	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
vg0124627219	NA	4.47E-07	mr1748	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
vg0124627219	NA	3.24E-17	mr1746_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
vg0124627219	NA	6.90E-08	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
vg0124627219	1.66E-06	3.68E-07	mr1957_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