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Detailed information for vg0432940473:

Variant ID: vg0432940473 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32940473
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCCTGTTTGGCACAGCTCCAGCTCTAGCTCCACCTCTCCTGGAGCTGGAGCTCAGCCAAACAGTTTCAGCTCCACCAAAACTGGGAGTGGAGTTGGGTG[G/A]
AGCTCTCTCACAAAATGAACTAGAGTTGTGGAGCTGGGTTTAGACAGCTCCACAACTCCACTCCAGACCCAACTCCTGAAGCTAAATTTAGGAGTTAGAG

Reverse complement sequence

CTCTAACTCCTAAATTTAGCTTCAGGAGTTGGGTCTGGAGTGGAGTTGTGGAGCTGTCTAAACCCAGCTCCACAACTCTAGTTCATTTTGTGAGAGAGCT[C/T]
CACCCAACTCCACTCCCAGTTTTGGTGGAGCTGAAACTGTTTGGCTGAGCTCCAGCTCCAGGAGAGGTGGAGCTAGAGCTGGAGCTGTGCCAAACAGGCC

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	31.10%	3.30%	0.55%	65.07%	NA
All Indica	2759	4.20%	0.10%	0.36%	95.29%	NA
All Japonica	1512	77.10%	9.70%	1.06%	12.17%	NA
Aus	269	43.10%	0.00%	0.00%	56.88%	NA
Indica I	595	7.40%	0.20%	0.34%	92.10%	NA
Indica II	465	3.90%	0.00%	0.00%	96.13%	NA
Indica III	913	0.90%	0.10%	0.55%	98.47%	NA
Indica Intermediate	786	6.00%	0.10%	0.38%	93.51%	NA
Temperate Japonica	767	91.90%	6.90%	0.52%	0.65%	NA
Tropical Japonica	504	61.50%	3.00%	2.18%	33.33%	NA
Japonica Intermediate	241	62.20%	32.80%	0.41%	4.56%	NA
VI/Aromatic	96	38.50%	0.00%	0.00%	61.46%	NA
Intermediate	90	40.00%	4.40%	0.00%	55.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0432940473	G -> DEL	N	N	silent_mutation	Average:60.977; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N
vg0432940473	G -> A	LOC_Os04g55360.1	upstream_gene_variant ; 3264.0bp to feature; MODIFIER	silent_mutation	Average:60.977; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N
vg0432940473	G -> A	LOC_Os04g55370.1	downstream_gene_variant ; 388.0bp to feature; MODIFIER	silent_mutation	Average:60.977; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N
vg0432940473	G -> A	LOC_Os04g55360-LOC_Os04g55370	intergenic_region ; MODIFIER	silent_mutation	Average:60.977; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432940473	1.08E-07	NA	mr1101	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
vg0432940473	6.13E-06	NA	mr1150	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
vg0432940473	NA	6.83E-06	mr1240	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