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Detailed information for vg0401321153:

Variant ID: vg0401321153 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1321153
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.83, A: 0.15, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

CGGTGTCCGTTGGTGAGAAGAAGGTGCCGCATTTTGAGCAACCTGTCGGCTGCTTCGAGCCTCCATGCCGCTAGCTTATAAGCTATGGCTGCCTGCTTCA[G/A]
ACAGGCTTAATTACCTGGCTGCAAGTATTAATATGTATAGTCATGAATAAGCATATGACTTGTTCGGTGTATATGCTAGTTGCTTGCTGTACTGATATTG

Reverse complement sequence

CAATATCAGTACAGCAAGCAACTAGCATATACACCGAACAAGTCATATGCTTATTCATGACTATACATATTAATACTTGCAGCCAGGTAATTAAGCCTGT[C/T]
TGAAGCAGGCAGCCATAGCTTATAAGCTAGCGGCATGGAGGCTCGAAGCAGCCGACAGGTTGCTCAAAATGCGGCACCTTCTTCTCACCAACGGACACCG

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	28.70%	20.30%	0.80%	50.21%	NA
All Indica	2759	29.70%	15.60%	0.94%	53.72%	NA
All Japonica	1512	32.50%	31.50%	0.60%	35.38%	NA
Aus	269	0.00%	8.20%	0.37%	91.45%	NA
Indica I	595	63.50%	8.10%	0.67%	27.73%	NA
Indica II	465	15.90%	26.90%	0.43%	56.77%	NA
Indica III	913	19.90%	16.60%	0.33%	63.09%	NA
Indica Intermediate	786	23.70%	13.50%	2.16%	60.69%	NA
Temperate Japonica	767	5.10%	51.20%	0.65%	43.02%	NA
Tropical Japonica	504	63.50%	4.80%	0.79%	30.95%	NA
Japonica Intermediate	241	54.80%	24.90%	0.00%	20.33%	NA
VI/Aromatic	96	19.80%	3.10%	1.04%	76.04%	NA
Intermediate	90	27.80%	30.00%	1.11%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401321153	G -> DEL	N	N	silent_mutation	Average:40.645; most accessible tissue: Callus, score: 88.829	N	N	N	N
vg0401321153	G -> A	LOC_Os04g03164.1	3_prime_UTR_variant ; 27.0bp to feature; MODIFIER	silent_mutation	Average:40.645; most accessible tissue: Callus, score: 88.829	N	N	N	N
vg0401321153	G -> A	LOC_Os04g03150.1	downstream_gene_variant ; 3191.0bp to feature; MODIFIER	silent_mutation	Average:40.645; most accessible tissue: Callus, score: 88.829	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401321153	NA	2.67E-06	mr1182	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0401321153	NA	2.19E-06	mr1282	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0401321153	NA	3.59E-07	mr1544_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0401321153	4.14E-07	NA	mr1836_2	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