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Detailed information for vg0130669327:

Variant ID: vg0130669327 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 30669327
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGGCTATTACCTATCAGTTAAGGTGTCCGAACCTATATAAAAATCCATATCCCCCATCTCTATTACTGTAATCTTGCGTATACCATAGTTCCAACGATCC[C/T]
CGTACTGTACAAGTCCAGTATGCGGGTATAGTTTGTCAACATATAGAACATAATACGAGATTAATTGAAAATTGAAATAAAAATAAAAAAGATCCCAAAA

Reverse complement sequence

TTTTGGGATCTTTTTTATTTTTATTTCAATTTTCAATTAATCTCGTATTATGTTCTATATGTTGACAAACTATACCCGCATACTGGACTTGTACAGTACG[G/A]
GGATCGTTGGAACTATGGTATACGCAAGATTACAGTAATAGAGATGGGGGATATGGATTTTTATATAGGTTCGGACACCTTAACTGATAGGTAATAGCCC

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	90.60%	6.40%	1.08%	1.90%	NA
All Indica	2759	87.40%	10.80%	1.81%	0.00%	NA
All Japonica	1512	94.10%	0.00%	0.00%	5.89%	NA
Aus	269	99.30%	0.40%	0.00%	0.37%	NA
Indica I	595	99.20%	0.00%	0.84%	0.00%	NA
Indica II	465	80.90%	16.10%	3.01%	0.00%	NA
Indica III	913	84.30%	13.90%	1.75%	0.00%	NA
Indica Intermediate	786	85.80%	12.30%	1.91%	0.00%	NA
Temperate Japonica	767	95.60%	0.00%	0.00%	4.43%	NA
Tropical Japonica	504	98.40%	0.00%	0.00%	1.59%	NA
Japonica Intermediate	241	80.50%	0.00%	0.00%	19.50%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	3.30%	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
vg0130669327	C -> T	LOC_Os01g53380.1	upstream_gene_variant ; 2205.0bp to feature; MODIFIER	silent_mutation	Average:52.907; most accessible tissue: Zhenshan97 flag leaf, score: 63.67	N	N	N	N
vg0130669327	C -> T	LOC_Os01g53370.1	downstream_gene_variant ; 696.0bp to feature; MODIFIER	silent_mutation	Average:52.907; most accessible tissue: Zhenshan97 flag leaf, score: 63.67	N	N	N	N
vg0130669327	C -> T	LOC_Os01g53370-LOC_Os01g53380	intergenic_region ; MODIFIER	silent_mutation	Average:52.907; most accessible tissue: Zhenshan97 flag leaf, score: 63.67	N	N	N	N
vg0130669327	C -> DEL	N	N	silent_mutation	Average:52.907; most accessible tissue: Zhenshan97 flag leaf, score: 63.67	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0130669327	4.07E-06	4.07E-06	mr1258	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