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Detailed information for vg0412484073:

Variant ID: vg0412484073 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12484073
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

GTCCGTGCCATCGAGGATGCCTGTGGAGTGGTGTTCCCGCTGTAGTTCAAGTCAAGGCTTAGCTCCAGTTATCTTTTGTTTTTCCGCTGCATTTATGTAA[A/G]
ACTTTTATAATGTTTGTAAGACGTGGATCTGTATGTCAACTTTGTCGTTTGTGTACCCCGGCCGGTCCTGGACGGGGATTTTAATGCACATTCTGCTTGG

Reverse complement sequence

CCAAGCAGAATGTGCATTAAAATCCCCGTCCAGGACCGGCCGGGGTACACAAACGACAAAGTTGACATACAGATCCACGTCTTACAAACATTATAAAAGT[T/C]
TTACATAAATGCAGCGGAAAAACAAAAGATAACTGGAGCTAAGCCTTGACTTGAACTACAGCGGGAACACCACTCCACAGGCATCCTCGATGGCACGGAC

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	50.60%	6.30%	5.40%	37.75%	NA
All Indica	2759	24.90%	9.60%	8.12%	57.41%	NA
All Japonica	1512	99.20%	0.20%	0.00%	0.60%	NA
Aus	269	21.20%	8.60%	9.29%	60.97%	NA
Indica I	595	48.10%	4.90%	3.87%	43.19%	NA
Indica II	465	26.20%	11.40%	8.17%	54.19%	NA
Indica III	913	6.60%	12.00%	10.62%	70.76%	NA
Indica Intermediate	786	27.90%	9.20%	8.40%	54.58%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	99.00%	0.20%	0.00%	0.79%	NA
Japonica Intermediate	241	97.90%	0.80%	0.00%	1.24%	NA
VI/Aromatic	96	92.70%	0.00%	2.08%	5.21%	NA
Intermediate	90	63.30%	7.80%	4.44%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412484073	A -> DEL	N	N	silent_mutation	Average:11.698; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0412484073	A -> G	LOC_Os04g22040.1	upstream_gene_variant ; 1773.0bp to feature; MODIFIER	silent_mutation	Average:11.698; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0412484073	A -> G	LOC_Os04g22030.1	downstream_gene_variant ; 3124.0bp to feature; MODIFIER	silent_mutation	Average:11.698; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0412484073	A -> G	LOC_Os04g22050.1	downstream_gene_variant ; 322.0bp to feature; MODIFIER	silent_mutation	Average:11.698; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0412484073	A -> G	LOC_Os04g22060.1	downstream_gene_variant ; 3368.0bp to feature; MODIFIER	silent_mutation	Average:11.698; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0412484073	A -> G	LOC_Os04g22040-LOC_Os04g22050	intergenic_region ; MODIFIER	silent_mutation	Average:11.698; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412484073	5.81E-09	4.35E-10	mr1071_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
vg0412484073	7.99E-06	NA	mr1080_2	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
vg0412484073	1.96E-08	2.12E-08	mr1080_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
vg0412484073	1.34E-07	NA	mr1203_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
vg0412484073	3.82E-06	NA	mr1613_2	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
vg0412484073	1.41E-07	3.52E-09	mr1613_2	Ind_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
vg0412484073	3.39E-06	NA	mr1619_2	Ind_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