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Detailed information for vg0316394110:

Variant ID: vg0316394110 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 16394110
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGCTACGTTATTTCTGTAGTCGTACCTCGACCATCTGAAGTTAAGGTGCGAGAGATTGCTACATTTTACTAGTTGATTGTGTCCCCTCTCCTCCTAGGGG[T/G]
CCTTGTATTTATACCCATAGGTGTCCCCTTGTTCAAGTAGAACTAGGGAAACCAATATGGATATAATTCGAGTAATCCTTGTCGTTTCCATGTAGAATTC

Reverse complement sequence

GAATTCTACATGGAAACGACAAGGATTACTCGAATTATATCCATATTGGTTTCCCTAGTTCTACTTGAACAAGGGGACACCTATGGGTATAAATACAAGG[A/C]
CCCCTAGGAGGAGAGGGGACACAATCAACTAGTAAAATGTAGCAATCTCTCGCACCTTAACTTCAGATGGTCGAGGTACGACTACAGAAATAACGTAGCG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	38.30%	5.40%	0.42%	55.88%	NA
All Indica	2759	20.80%	3.60%	0.47%	75.17%	NA
All Japonica	1512	68.80%	9.20%	0.33%	21.63%	NA
Aus	269	27.10%	3.70%	0.00%	69.14%	NA
Indica I	595	40.00%	2.20%	0.84%	56.97%	NA
Indica II	465	9.90%	0.00%	0.43%	89.68%	NA
Indica III	913	11.60%	6.50%	0.11%	81.82%	NA
Indica Intermediate	786	23.30%	3.40%	0.64%	72.65%	NA
Temperate Japonica	767	95.20%	4.00%	0.26%	0.52%	NA
Tropical Japonica	504	35.50%	3.80%	0.60%	60.12%	NA
Japonica Intermediate	241	54.80%	36.90%	0.00%	8.30%	NA
VI/Aromatic	96	87.50%	2.10%	0.00%	10.42%	NA
Intermediate	90	44.40%	4.40%	2.22%	48.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0316394110	T -> DEL	N	N	silent_mutation	Average:24.441; most accessible tissue: Zhenshan97 root, score: 56.557	N	N	N	N
vg0316394110	T -> G	LOC_Os03g28910.1	downstream_gene_variant ; 3136.0bp to feature; MODIFIER	silent_mutation	Average:24.441; most accessible tissue: Zhenshan97 root, score: 56.557	N	N	N	N
vg0316394110	T -> G	LOC_Os03g28410-LOC_Os03g28910	intergenic_region ; MODIFIER	silent_mutation	Average:24.441; most accessible tissue: Zhenshan97 root, score: 56.557	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0316394110	3.34E-06	3.34E-06	mr1578	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
vg0316394110	NA	4.46E-06	mr1240_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251