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Detailed information for vg0414315785:

Variant ID: vg0414315785 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 14315785
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAACTATTAGATTGCTTTTCTCTTTATAAAAAAAACTTTAAGCCACCACATGTCATGTCTTAAAGATCCTTAGAATGAGAAAACAACAAATCATAGGTTC[G/T]
CACTTAGATTGTTTACAAAGATTTTCTTTTTAAAAAAACAATGTACCGTCCACTTCCCCTCCCTGTCCAATCATATGCACATAACACTATTGCATTGTGA

Reverse complement sequence

TCACAATGCAATAGTGTTATGTGCATATGATTGGACAGGGAGGGGAAGTGGACGGTACATTGTTTTTTTAAAAAGAAAATCTTTGTAAACAATCTAAGTG[C/A]
GAACCTATGATTTGTTGTTTTCTCATTCTAAGGATCTTTAAGACATGACATGTGGTGGCTTAAAGTTTTTTTTATAAAGAGAAAAGCAATCTAATAGTTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.30%	12.90%	6.60%	27.19%	NA
All Indica	2759	54.70%	18.20%	6.81%	20.26%	NA
All Japonica	1512	43.70%	4.00%	6.88%	45.44%	NA
Aus	269	95.50%	2.60%	1.49%	0.37%	NA
Indica I	595	54.30%	5.40%	5.04%	35.29%	NA
Indica II	465	86.00%	6.00%	2.58%	5.38%	NA
Indica III	913	36.40%	35.30%	10.08%	18.29%	NA
Indica Intermediate	786	57.90%	15.30%	6.87%	19.97%	NA
Temperate Japonica	767	75.50%	0.40%	1.56%	22.56%	NA
Tropical Japonica	504	3.80%	5.60%	12.10%	78.57%	NA
Japonica Intermediate	241	26.10%	12.00%	12.86%	48.96%	NA
VI/Aromatic	96	39.60%	29.20%	10.42%	20.83%	NA
Intermediate	90	61.10%	12.20%	6.67%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0414315785	G -> DEL	N	N	silent_mutation	Average:15.554; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0414315785	G -> T	LOC_Os04g24850.1	upstream_gene_variant ; 2496.0bp to feature; MODIFIER	silent_mutation	Average:15.554; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0414315785	G -> T	LOC_Os04g24850-LOC_Os04g24860	intergenic_region ; MODIFIER	silent_mutation	Average:15.554; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0414315785	3.34E-06	3.33E-06	mr1673	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