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Detailed information for vg0514388692:

Variant ID: vg0514388692 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 14388692
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTAAAATATATTAAATGGTGGGCTGTGGGTACATGGTTCTGTTGGTCGCGCCCATGGCAATTAAGGACCGGTTCGCGGGAAACCCTGGAAGAATTCCTC[G/A]
TACTTACCACAAGCCAGCATGGGCAACTGCTGGGCTTGTAGTGTAGCTTTCCTCTAGCTGACGCATCCAGGCAAGGGTGGGCGTGATGGAGCGGGATGGG

Reverse complement sequence

CCCATCCCGCTCCATCACGCCCACCCTTGCCTGGATGCGTCAGCTAGAGGAAAGCTACACTACAAGCCCAGCAGTTGCCCATGCTGGCTTGTGGTAAGTA[C/T]
GAGGAATTCTTCCAGGGTTTCCCGCGAACCGGTCCTTAATTGCCATGGGCGCGACCAACAGAACCATGTACCCACAGCCCACCATTTAATATATTTTAAT

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	95.50%	2.90%	1.59%	0.00%	NA
All Indica	2759	99.80%	0.10%	0.07%	0.00%	NA
All Japonica	1512	86.60%	8.70%	4.76%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	99.20%	0.50%	0.34%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	75.00%	16.60%	8.47%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	95.90%	1.70%	2.49%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0514388692	G -> A	LOC_Os05g24810.1	downstream_gene_variant ; 2425.0bp to feature; MODIFIER	silent_mutation	Average:55.862; most accessible tissue: Zhenshan97 flag leaf, score: 77.738	N	N	N	N
vg0514388692	G -> A	LOC_Os05g24820.1	downstream_gene_variant ; 525.0bp to feature; MODIFIER	silent_mutation	Average:55.862; most accessible tissue: Zhenshan97 flag leaf, score: 77.738	N	N	N	N
vg0514388692	G -> A	LOC_Os05g24810-LOC_Os05g24820	intergenic_region ; MODIFIER	silent_mutation	Average:55.862; most accessible tissue: Zhenshan97 flag leaf, score: 77.738	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0514388692	3.51E-06	1.46E-09	mr1627_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
vg0514388692	8.20E-06	8.20E-06	mr1895_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