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Detailed information for vg0207302554:

Variant ID: vg0207302554 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 7302554
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATTCTGGCTTAGATTTCTTAGTGGCATGTAAAACAAAACAAGTCAATAATGTAGAATTAATTGTGTATTAATTATTATTGTTCGGGTTATGGATACCAC[A/G]
TACCTAATAGTAATTGACTAAATCTCGGCAGGACCCATCACATACCATGTCTTATATGGAAACTGACCTCAGATATGGAGGGAGTTCCGGATAAGGAAAG

Reverse complement sequence

CTTTCCTTATCCGGAACTCCCTCCATATCTGAGGTCAGTTTCCATATAAGACATGGTATGTGATGGGTCCTGCCGAGATTTAGTCAATTACTATTAGGTA[T/C]
GTGGTATCCATAACCCGAACAATAATAATTAATACACAATTAATTCTACATTATTGACTTGTTTTGTTTTACATGCCACTAAGAAATCTAAGCCAGAATT

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	84.00%	6.60%	1.71%	7.64%	NA
All Indica	2759	84.40%	0.00%	2.72%	12.87%	NA
All Japonica	1512	79.20%	20.20%	0.33%	0.20%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	81.80%	0.00%	6.55%	11.60%	NA
Indica II	465	80.90%	0.00%	2.80%	16.34%	NA
Indica III	913	85.30%	0.00%	0.88%	13.80%	NA
Indica Intermediate	786	87.40%	0.00%	1.91%	10.69%	NA
Temperate Japonica	767	77.30%	21.90%	0.52%	0.26%	NA
Tropical Japonica	504	84.30%	15.50%	0.00%	0.20%	NA
Japonica Intermediate	241	74.70%	24.90%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	7.80%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0207302554	A -> G	LOC_Os02g13590.1	downstream_gene_variant ; 2527.0bp to feature; MODIFIER	silent_mutation	Average:67.369; most accessible tissue: Callus, score: 90.355	N	N	N	N
vg0207302554	A -> G	LOC_Os02g13600.1	downstream_gene_variant ; 881.0bp to feature; MODIFIER	silent_mutation	Average:67.369; most accessible tissue: Callus, score: 90.355	N	N	N	N
vg0207302554	A -> G	LOC_Os02g13610.1	downstream_gene_variant ; 539.0bp to feature; MODIFIER	silent_mutation	Average:67.369; most accessible tissue: Callus, score: 90.355	N	N	N	N
vg0207302554	A -> G	LOC_Os02g13600-LOC_Os02g13610	intergenic_region ; MODIFIER	silent_mutation	Average:67.369; most accessible tissue: Callus, score: 90.355	N	N	N	N
vg0207302554	A -> DEL	N	N	silent_mutation	Average:67.369; most accessible tissue: Callus, score: 90.355	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0207302554	NA	8.15E-07	mr1201_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
vg0207302554	2.56E-06	NA	mr1219_2	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
vg0207302554	NA	1.75E-07	mr1219_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
vg0207302554	NA	6.33E-06	mr1274_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