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Detailed information for vg0408346647:

Variant ID: vg0408346647 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 8346647
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTAGAACTGATATGTCTTTGAAGCAAGCACGCAGCAAGTAGTGGCATAGATTAACTTGTTGAGTTTCATCAACAAAACATATGCATCGGTCATGTATCT[C/G]
TATTTCTGCCAAATCTTTGCTGTAATGCCTGCTTACCACAATTGGTTATTGAAAAAATGCATTACAATTTAGCAATACCCAGCTTACATTCCTTTTCTTC

Reverse complement sequence

GAAGAAAAGGAATGTAAGCTGGGTATTGCTAAATTGTAATGCATTTTTTCAATAACCAATTGTGGTAAGCAGGCATTACAGCAAAGATTTGGCAGAAATA[G/C]
AGATACATGACCGATGCATATGTTTTGTTGATGAAACTCAACAAGTTAATCTATGCCACTACTTGCTGCGTGCTTGCTTCAAAGACATATCAGTTCTAAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	25.20%	8.00%	0.57%	66.23%	NA
All Indica	2759	7.80%	7.60%	0.87%	83.69%	NA
All Japonica	1512	62.80%	0.30%	0.07%	36.84%	NA
Aus	269	2.20%	52.00%	0.37%	45.35%	NA
Indica I	595	14.50%	0.20%	1.68%	83.70%	NA
Indica II	465	5.40%	21.90%	0.65%	72.04%	NA
Indica III	913	3.50%	6.50%	0.33%	89.70%	NA
Indica Intermediate	786	9.20%	6.20%	1.02%	83.59%	NA
Temperate Japonica	767	96.00%	0.10%	0.00%	3.91%	NA
Tropical Japonica	504	8.70%	0.60%	0.20%	90.48%	NA
Japonica Intermediate	241	70.10%	0.40%	0.00%	29.46%	NA
VI/Aromatic	96	0.00%	13.50%	0.00%	86.46%	NA
Intermediate	90	25.60%	7.80%	1.11%	65.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0408346647	C -> DEL	N	N	silent_mutation	Average:8.341; most accessible tissue: Callus, score: 38.694	N	N	N	N
vg0408346647	C -> G	LOC_Os04g14850.1	downstream_gene_variant ; 4414.0bp to feature; MODIFIER	silent_mutation	Average:8.341; most accessible tissue: Callus, score: 38.694	N	N	N	N
vg0408346647	C -> G	LOC_Os04g14840.1	intron_variant ; MODIFIER	silent_mutation	Average:8.341; most accessible tissue: Callus, score: 38.694	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0408346647	NA	6.99E-06	mr1081	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
vg0408346647	NA	1.16E-06	mr1761	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