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Detailed information for vg0315191994:

Variant ID: vg0315191994 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 15191994
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATTTAAATATAGGATCAACATGCTCAAAGGAATTGTGTTTGGGATCTGTGTGACTTGCCTTGCAACATTCGGTCTTCAATTAATCTTCTTGAACACTTC[C/T]
GGCGCACTTGCGAACCTTCGAAACGACGGAAACGACAAGCTAACACGCAAAACGAGGAAAAATACTAAGAAACTCCAAATAAACAATACATATAAAGTAA

Reverse complement sequence

TTACTTTATATGTATTGTTTATTTGGAGTTTCTTAGTATTTTTCCTCGTTTTGCGTGTTAGCTTGTCGTTTCCGTCGTTTCGAAGGTTCGCAAGTGCGCC[G/A]
GAAGTGTTCAAGAAGATTAATTGAAGACCGAATGTTGCAAGGCAAGTCACACAGATCCCAAACACAATTCCTTTGAGCATGTTGATCCTATATTTAAATT

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	87.80%	6.80%	4.85%	0.55%	NA
All Indica	2759	81.00%	11.50%	7.50%	0.07%	NA
All Japonica	1512	97.60%	0.00%	0.99%	1.46%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	89.10%	2.00%	8.91%	0.00%	NA
Indica II	465	90.50%	1.70%	7.74%	0.00%	NA
Indica III	913	68.80%	25.10%	6.13%	0.00%	NA
Indica Intermediate	786	83.30%	8.50%	7.89%	0.25%	NA
Temperate Japonica	767	98.60%	0.00%	0.65%	0.78%	NA
Tropical Japonica	504	99.20%	0.00%	0.60%	0.20%	NA
Japonica Intermediate	241	90.90%	0.00%	2.90%	6.22%	NA
VI/Aromatic	96	94.80%	3.10%	1.04%	1.04%	NA
Intermediate	90	91.10%	2.20%	5.56%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0315191994	C -> T	LOC_Os03g26590.1	intron_variant ; MODIFIER	silent_mutation	Average:21.228; most accessible tissue: Minghui63 flower, score: 39.047	N	N	N	N
vg0315191994	C -> DEL	N	N	silent_mutation	Average:21.228; most accessible tissue: Minghui63 flower, score: 39.047	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0315191994	1.00E-06	1.70E-06	mr1084	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