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Detailed information for vg0331773900:

Variant ID: vg0331773900 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 31773900
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTAGTTGAATTTTTTTCTTTTTCTAATTTCAGAATTTATTTTATTTATTATTATGTTCTTTTGATATTTTTATTTTTTATTTTCAATCGCAGTTGTTTCA[A/T]
AATTGTATTCCTACTTTAACTCTCTTTTTAATTTGCCTAATTTCAGATTATTTATTTATTTATTATTAGAAATTTTAATTAATCTGCTATTGGGTTCTTA

Reverse complement sequence

TAAGAACCCAATAGCAGATTAATTAAAATTTCTAATAATAAATAAATAAATAATCTGAAATTAGGCAAATTAAAAAGAGAGTTAAAGTAGGAATACAATT[T/A]
TGAAACAACTGCGATTGAAAATAAAAAATAAAAATATCAAAAGAACATAATAATAAATAAAATAAATTCTGAAATTAGAAAAAGAAAAAAATTCAACTAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.40%	0.10%	2.05%	0.36%	NA
All Indica	2759	95.70%	0.30%	3.48%	0.62%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	93.40%	0.50%	5.38%	0.67%	NA
Indica II	465	94.00%	0.00%	5.16%	0.86%	NA
Indica III	913	98.00%	0.20%	1.10%	0.66%	NA
Indica Intermediate	786	95.50%	0.30%	3.82%	0.38%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg0331773900	A -> T	LOC_Os03g55810.1	downstream_gene_variant ; 2060.0bp to feature; MODIFIER	silent_mutation	Average:23.841; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0331773900	A -> T	LOC_Os03g55820.1	downstream_gene_variant ; 4371.0bp to feature; MODIFIER	silent_mutation	Average:23.841; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0331773900	A -> T	LOC_Os03g55800-LOC_Os03g55810	intergenic_region ; MODIFIER	silent_mutation	Average:23.841; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0331773900	A -> DEL	N	N	silent_mutation	Average:23.841; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0331773900	4.16E-06	NA	mr1027_2	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