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Detailed information for vg0329978728:

Variant ID: vg0329978728 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 29978728
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAAAATTTGAATTTTAAAATATAAGAAATTCAAATAATTTTTCGGGTAGTAAATGATTTCAAATGGGAAAGTTGTCAACACCAAAGTTGTATAACTTAT[C/T]
AAGATCTACAACTTTTGTTTTGGTCATTTTTCTATATGACTTTGTTTGAACAATTTTGAATTTGAATTTTAAATTATGACAACTTCAAACAACATTTACA

Reverse complement sequence

TGTAAATGTTGTTTGAAGTTGTCATAATTTAAAATTCAAATTCAAAATTGTTCAAACAAAGTCATATAGAAAAATGACCAAAACAAAAGTTGTAGATCTT[G/A]
ATAAGTTATACAACTTTGGTGTTGACAACTTTCCCATTTGAAATCATTTACTACCCGAAAAATTATTTGAATTTCTTATATTTTAAAATTCAAATTTTAT

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	94.40%	0.30%	0.63%	4.68%	NA
All Indica	2759	91.40%	0.20%	0.80%	7.58%	NA
All Japonica	1512	99.50%	0.30%	0.20%	0.00%	NA
Aus	269	94.80%	1.50%	1.12%	2.60%	NA
Indica I	595	90.60%	0.20%	0.50%	8.74%	NA
Indica II	465	84.70%	0.00%	1.29%	13.98%	NA
Indica III	913	94.00%	0.30%	0.55%	5.15%	NA
Indica Intermediate	786	93.10%	0.10%	1.02%	5.73%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	0.80%	0.60%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	93.30%	0.00%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0329978728	C -> T	LOC_Os03g52210.1	upstream_gene_variant ; 4238.0bp to feature; MODIFIER	silent_mutation	Average:21.959; most accessible tissue: Callus, score: 47.207	N	N	N	N
vg0329978728	C -> T	LOC_Os03g52230.1	upstream_gene_variant ; 798.0bp to feature; MODIFIER	silent_mutation	Average:21.959; most accessible tissue: Callus, score: 47.207	N	N	N	N
vg0329978728	C -> T	LOC_Os03g52230-LOC_Os03g52239	intergenic_region ; MODIFIER	silent_mutation	Average:21.959; most accessible tissue: Callus, score: 47.207	N	N	N	N
vg0329978728	C -> DEL	N	N	silent_mutation	Average:21.959; most accessible tissue: Callus, score: 47.207	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0329978728	2.95E-06	NA	mr1542	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