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Detailed information for vg0714836122:

Variant ID: vg0714836122 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14836122
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATACAAAACAGAAATACCACTGAACATCTATACCCTTAACAATATATTGGCCAAATTACTCATGCAGATATCGAATTTTGGCCTTGATTTTCCGTTGCA[A/G]
TCTTTATTCTCATGCAGGTTTGGTATATCCTGTTCAATGATAACGTACCTTTCAAGATCCACTAGCCTTTACATTATGATATTCAGATTAATGGTATGTG

Reverse complement sequence

CACATACCATTAATCTGAATATCATAATGTAAAGGCTAGTGGATCTTGAAAGGTACGTTATCATTGAACAGGATATACCAAACCTGCATGAGAATAAAGA[T/C]
TGCAACGGAAAATCAAGGCCAAAATTCGATATCTGCATGAGTAATTTGGCCAATATATTGTTAAGGGTATAGATGTTCAGTGGTATTTCTGTTTTGTATA

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	38.80%	7.40%	1.27%	52.58%	NA
All Indica	2759	6.40%	11.60%	1.92%	80.10%	NA
All Japonica	1512	99.10%	0.00%	0.00%	0.93%	NA
Aus	269	10.00%	10.00%	2.23%	77.70%	NA
Indica I	595	4.40%	29.70%	2.02%	63.87%	NA
Indica II	465	5.60%	6.00%	2.58%	85.81%	NA
Indica III	913	2.40%	1.30%	1.64%	94.63%	NA
Indica Intermediate	786	13.10%	13.00%	1.78%	72.14%	NA
Temperate Japonica	767	99.00%	0.00%	0.00%	1.04%	NA
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	85.40%	0.00%	0.00%	14.58%	NA
Intermediate	90	53.30%	3.30%	1.11%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714836122	A -> DEL	N	N	silent_mutation	Average:9.398; most accessible tissue: Callus, score: 38.829	N	N	N	N
vg0714836122	A -> G	LOC_Os07g25830.1	downstream_gene_variant ; 4809.0bp to feature; MODIFIER	silent_mutation	Average:9.398; most accessible tissue: Callus, score: 38.829	N	N	N	N
vg0714836122	A -> G	LOC_Os07g25840.1	downstream_gene_variant ; 618.0bp to feature; MODIFIER	silent_mutation	Average:9.398; most accessible tissue: Callus, score: 38.829	N	N	N	N
vg0714836122	A -> G	LOC_Os07g25830-LOC_Os07g25840	intergenic_region ; MODIFIER	silent_mutation	Average:9.398; most accessible tissue: Callus, score: 38.829	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714836122	NA	8.43E-06	mr1045_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
vg0714836122	4.64E-06	1.62E-07	mr1198_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