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Detailed information for vg0115927658:

Variant ID: vg0115927658 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 15927658
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGCAACATACAAAAAGATGTATTAGGATAAACGCGAAGTAACATATATTGCATTTGACGTTCACGTTTCGTTCACAATCGTTCACATTCGCGTTCTCGTT[A/C]
AGGTCACGTTTCATTCACCTACGTTCGTTCGTTCACGTTCATTCACCTACATATATTGTATTTCACGTTCACGTTCGTTCACGTTCACGTTCGTTCGTTC

Reverse complement sequence

GAACGAACGAACGTGAACGTGAACGAACGTGAACGTGAAATACAATATATGTAGGTGAATGAACGTGAACGAACGAACGTAGGTGAATGAAACGTGACCT[T/G]
AACGAGAACGCGAATGTGAACGATTGTGAACGAAACGTGAACGTCAAATGCAATATATGTTACTTCGCGTTTATCCTAATACATCTTTTTGTATGTTGCA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	40.60%	0.30%	0.51%	58.57%	NA
All Indica	2759	7.10%	0.50%	0.87%	91.52%	NA
All Japonica	1512	97.40%	0.00%	0.00%	2.65%	NA
Aus	269	39.40%	0.00%	0.00%	60.59%	NA
Indica I	595	2.90%	0.30%	1.18%	95.63%	NA
Indica II	465	16.30%	0.20%	1.08%	82.37%	NA
Indica III	913	2.80%	0.80%	0.33%	96.06%	NA
Indica Intermediate	786	9.70%	0.60%	1.15%	88.55%	NA
Temperate Japonica	767	99.00%	0.00%	0.00%	1.04%	NA
Tropical Japonica	504	94.60%	0.00%	0.00%	5.36%	NA
Japonica Intermediate	241	97.90%	0.00%	0.00%	2.07%	NA
VI/Aromatic	96	93.80%	0.00%	0.00%	6.25%	NA
Intermediate	90	62.20%	0.00%	0.00%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0115927658	A -> DEL	N	N	silent_mutation	Average:13.512; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N
vg0115927658	A -> C	LOC_Os01g28420.1	upstream_gene_variant ; 1087.0bp to feature; MODIFIER	silent_mutation	Average:13.512; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N
vg0115927658	A -> C	LOC_Os01g28440.1	downstream_gene_variant ; 1605.0bp to feature; MODIFIER	silent_mutation	Average:13.512; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N
vg0115927658	A -> C	LOC_Os01g28420-LOC_Os01g28440	intergenic_region ; MODIFIER	silent_mutation	Average:13.512; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0115927658	1.45E-06	NA	mr1261	Ind_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