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Detailed information for vg0503396062:

Variant ID: vg0503396062 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 3396062
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGGAGCTTCTACTTCGACCAAGAATATTAAGAATCATTGTTTAGCTCCTAGAAAACAACCACAGCCGAAGTGGATACCTTCTGGCTTATCTCGTTCTCA[G/A]
AAGAGGAGGTTACAACGTCTTCGGGCCATAGGTAAAAAAGAAAAGGAGGCCGAAGATGTAGAGAACAAAACATGTAATAATTTAGAGCCTCGAACGACAC

Reverse complement sequence

GTGTCGTTCGAGGCTCTAAATTATTACATGTTTTGTTCTCTACATCTTCGGCCTCCTTTTCTTTTTTACCTATGGCCCGAAGACGTTGTAACCTCCTCTT[C/T]
TGAGAACGAGATAAGCCAGAAGGTATCCACTTCGGCTGTGGTTGTTTTCTAGGAGCTAAACAATGATTCTTAATATTCTTGGTCGAAGTAGAAGCTCCTA

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	80.60%	0.20%	2.33%	16.89%	NA
All Indica	2759	70.60%	0.20%	3.48%	25.73%	NA
All Japonica	1512	93.80%	0.10%	0.73%	5.36%	NA
Aus	269	98.50%	0.40%	0.00%	1.12%	NA
Indica I	595	36.50%	0.20%	4.03%	59.33%	NA
Indica II	465	79.10%	0.20%	4.73%	15.91%	NA
Indica III	913	87.60%	0.20%	2.63%	9.53%	NA
Indica Intermediate	786	71.50%	0.30%	3.31%	24.94%	NA
Temperate Japonica	767	93.60%	0.00%	0.78%	5.61%	NA
Tropical Japonica	504	99.20%	0.20%	0.40%	0.20%	NA
Japonica Intermediate	241	83.40%	0.00%	1.24%	15.35%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	0.00%	3.33%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0503396062	G -> DEL	N	N	silent_mutation	Average:37.947; most accessible tissue: Minghui63 young leaf, score: 68.07	N	N	N	N
vg0503396062	G -> A	LOC_Os05g06570.1	downstream_gene_variant ; 183.0bp to feature; MODIFIER	silent_mutation	Average:37.947; most accessible tissue: Minghui63 young leaf, score: 68.07	N	N	N	N
vg0503396062	G -> A	LOC_Os05g06580.1	downstream_gene_variant ; 2908.0bp to feature; MODIFIER	silent_mutation	Average:37.947; most accessible tissue: Minghui63 young leaf, score: 68.07	N	N	N	N
vg0503396062	G -> A	LOC_Os05g06570-LOC_Os05g06580	intergenic_region ; MODIFIER	silent_mutation	Average:37.947; most accessible tissue: Minghui63 young leaf, score: 68.07	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0503396062	1.55E-06	NA	mr1933	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
vg0503396062	2.37E-09	2.38E-09	mr1957	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
vg0503396062	1.35E-06	1.35E-06	mr1957	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