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Detailed information for vg0402536732:

Variant ID: vg0402536732 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2536732
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

AGATATGCAGTAGAAGCGTAGAATATAATGTTCATATTCGACAGAAAAATCAAGTGAAACGAAACTAAGAGAGGCGAGAAGAAGGCAATATACACGTACC[G/A]
GCGAACGGGTCTAGACCAAAATAATCGATGAATTTACCGGTCCCTCTGGCTTGAACTGACTGACTGTCTCCCAATTAAGCTCCTATTATACTGGAGTGGA

Reverse complement sequence

TCCACTCCAGTATAATAGGAGCTTAATTGGGAGACAGTCAGTCAGTTCAAGCCAGAGGGACCGGTAAATTCATCGATTATTTTGGTCTAGACCCGTTCGC[C/T]
GGTACGTGTATATTGCCTTCTTCTCGCCTCTCTTAGTTTCGTTTCACTTGATTTTTCTGTCGAATATGAACATTATATTCTACGCTTCTACTGCATATCT

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	74.20%	12.60%	2.60%	10.62%	NA
All Indica	2759	74.60%	14.00%	0.91%	10.51%	NA
All Japonica	1512	76.50%	5.00%	6.22%	12.37%	NA
Aus	269	48.00%	46.50%	0.37%	5.20%	NA
Indica I	595	94.30%	0.00%	0.00%	5.71%	NA
Indica II	465	82.20%	15.30%	0.43%	2.15%	NA
Indica III	913	63.90%	21.80%	1.20%	13.14%	NA
Indica Intermediate	786	67.70%	14.80%	1.53%	16.03%	NA
Temperate Japonica	767	89.40%	1.40%	5.61%	3.52%	NA
Tropical Japonica	504	68.10%	3.40%	5.75%	22.82%	NA
Japonica Intermediate	241	52.70%	19.50%	9.13%	18.67%	NA
VI/Aromatic	96	92.70%	2.10%	1.04%	4.17%	NA
Intermediate	90	83.30%	6.70%	2.22%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402536732	G -> DEL	N	N	silent_mutation	Average:63.12; most accessible tissue: Zhenshan97 young leaf, score: 83.412	N	N	N	N
vg0402536732	G -> A	LOC_Os04g05104.1	upstream_gene_variant ; 1443.0bp to feature; MODIFIER	silent_mutation	Average:63.12; most accessible tissue: Zhenshan97 young leaf, score: 83.412	N	N	N	N
vg0402536732	G -> A	LOC_Os04g05120.1	downstream_gene_variant ; 3302.0bp to feature; MODIFIER	silent_mutation	Average:63.12; most accessible tissue: Zhenshan97 young leaf, score: 83.412	N	N	N	N
vg0402536732	G -> A	LOC_Os04g05104-LOC_Os04g05120	intergenic_region ; MODIFIER	silent_mutation	Average:63.12; most accessible tissue: Zhenshan97 young leaf, score: 83.412	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402536732	1.57E-06	NA	mr1155_2	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