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Detailed information for vg0405034359:

Variant ID: vg0405034359 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 5034359
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.00, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

CGTCACCCCATACTCGGTAACACACGACACCACCCAGAAGTTGTCGTCTATCTAGCTAATATAGTCGTTGATCTATGAATATATTAACACACTTGTCATC[A/G]
CCGATCTTATGGATCAGCGCGCTTGGGACACTGTTGATTGTGACTTGTATGTTAATCCGTCATATTGCTATCTGTATGAAGTAGATGGTAACAAATCCGA

Reverse complement sequence

TCGGATTTGTTACCATCTACTTCATACAGATAGCAATATGACGGATTAACATACAAGTCACAATCAACAGTGTCCCAAGCGCGCTGATCCATAAGATCGG[T/C]
GATGACAAGTGTGTTAATATATTCATAGATCAACGACTATATTAGCTAGATAGACGACAACTTCTGGGTGGTGTCGTGTGTTACCGAGTATGGGGTGACG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.60%	5.90%	0.70%	2.86%	NA
All Indica	2759	95.10%	1.50%	0.72%	2.68%	NA
All Japonica	1512	80.40%	14.90%	0.86%	3.84%	NA
Aus	269	98.10%	1.50%	0.00%	0.37%	NA
Indica I	595	99.30%	0.00%	0.17%	0.50%	NA
Indica II	465	88.40%	5.20%	1.51%	4.95%	NA
Indica III	913	96.20%	0.80%	0.55%	2.52%	NA
Indica Intermediate	786	94.50%	1.40%	0.89%	3.18%	NA
Temperate Japonica	767	93.60%	6.30%	0.00%	0.13%	NA
Tropical Japonica	504	71.80%	14.50%	2.38%	11.31%	NA
Japonica Intermediate	241	56.00%	43.60%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	5.60%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0405034359	A -> DEL	N	N	silent_mutation	Average:26.431; most accessible tissue: Zhenshan97 flag leaf, score: 65.3	N	N	N	N
vg0405034359	A -> G	LOC_Os04g09420.1	downstream_gene_variant ; 219.0bp to feature; MODIFIER	silent_mutation	Average:26.431; most accessible tissue: Zhenshan97 flag leaf, score: 65.3	N	N	N	N
vg0405034359	A -> G	LOC_Os04g09410-LOC_Os04g09420	intergenic_region ; MODIFIER	silent_mutation	Average:26.431; most accessible tissue: Zhenshan97 flag leaf, score: 65.3	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0405034359	NA	1.46E-07	mr1622	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