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Detailed information for vg0517199333:

Variant ID: vg0517199333 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 17199333
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:

CTTCCTTTCTTAAATGTTTCACGCCGTTAACTTTTTAAAACATGTTTGACCGTTCATCTTATTTAAAAACTTTCGTGAAATGTGTAAAACTATATGAAAA[G/A]
TATATTTAACAATATGTATACATAAAAGTATATTTAACAATAAATCAAATGATAGGAAAAAAATTAATAATTACTTAAATTTTTTTGAATAAGACGAACG

Reverse complement sequence

CGTTCGTCTTATTCAAAAAAATTTAAGTAATTATTAATTTTTTTCCTATCATTTGATTTATTGTTAAATATACTTTTATGTATACATATTGTTAAATATA[C/T]
TTTTCATATAGTTTTACACATTTCACGAAAGTTTTTAAATAAGATGAACGGTCAAACATGTTTTAAAAAGTTAACGGCGTGAAACATTTAAGAAAGGAAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.40%	0.60%	1.74%	51.27%	NA
All Indica	2759	21.80%	0.00%	1.74%	76.44%	NA
All Japonica	1512	88.00%	1.50%	1.59%	8.93%	NA
Aus	269	43.90%	0.00%	3.35%	52.79%	NA
Indica I	595	32.90%	0.00%	1.68%	65.38%	NA
Indica II	465	14.40%	0.00%	3.23%	82.37%	NA
Indica III	913	18.20%	0.10%	0.77%	80.94%	NA
Indica Intermediate	786	21.90%	0.00%	2.04%	76.08%	NA
Temperate Japonica	767	93.10%	1.80%	2.22%	2.87%	NA
Tropical Japonica	504	77.80%	1.20%	0.99%	20.04%	NA
Japonica Intermediate	241	92.90%	1.20%	0.83%	4.98%	NA
VI/Aromatic	96	96.90%	1.00%	1.04%	1.04%	NA
Intermediate	90	58.90%	1.10%	0.00%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0517199333	G -> DEL	N	N	silent_mutation	Average:59.16; most accessible tissue: Minghui63 root, score: 70.803	N	N	N	N
vg0517199333	G -> A	LOC_Os05g29730.1	upstream_gene_variant ; 3731.0bp to feature; MODIFIER	silent_mutation	Average:59.16; most accessible tissue: Minghui63 root, score: 70.803	N	N	N	N
vg0517199333	G -> A	LOC_Os05g29740.1	upstream_gene_variant ; 312.0bp to feature; MODIFIER	silent_mutation	Average:59.16; most accessible tissue: Minghui63 root, score: 70.803	N	N	N	N
vg0517199333	G -> A	LOC_Os05g29750.1	upstream_gene_variant ; 3107.0bp to feature; MODIFIER	silent_mutation	Average:59.16; most accessible tissue: Minghui63 root, score: 70.803	N	N	N	N
vg0517199333	G -> A	LOC_Os05g29735.1	downstream_gene_variant ; 686.0bp to feature; MODIFIER	silent_mutation	Average:59.16; most accessible tissue: Minghui63 root, score: 70.803	N	N	N	N
vg0517199333	G -> A	LOC_Os05g29735-LOC_Os05g29740	intergenic_region ; MODIFIER	silent_mutation	Average:59.16; most accessible tissue: Minghui63 root, score: 70.803	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0517199333	1.23E-06	1.23E-06	mr1024	Jap_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