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Detailed information for vg0703978231:

Variant ID: vg0703978231 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 3978231
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGTATGTCCCCCATGAAAAATGTAGTGGCTGTGTAAACTGTAAAGTGGATCATGATACAAGTCAGGTCAAACGATAGCTTCAATATTTAAAAAAATGTA[A/G]
TACTATCTCTATATTTTAATGTATGACGCCGTTGATTTTTAATCAAACGTTTAACCATTTATTTTATTCAAAAAAATTTATGTAATTATCATTTTATTTT

Reverse complement sequence

AAAATAAAATGATAATTACATAAATTTTTTTGAATAAAATAAATGGTTAAACGTTTGATTAAAAATCAACGGCGTCATACATTAAAATATAGAGATAGTA[T/C]
TACATTTTTTTAAATATTGAAGCTATCGTTTGACCTGACTTGTATCATGATCCACTTTACAGTTTACACAGCCACTACATTTTTCATGGGGGACATACTT

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	82.60%	16.90%	0.49%	0.00%	NA
All Indica	2759	98.80%	1.10%	0.11%	0.00%	NA
All Japonica	1512	69.20%	29.90%	0.93%	0.00%	NA
Aus	269	20.80%	77.30%	1.86%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.60%	0.20%	0.22%	0.00%	NA
Indica III	913	99.10%	0.90%	0.00%	0.00%	NA
Indica Intermediate	786	97.30%	2.40%	0.25%	0.00%	NA
Temperate Japonica	767	96.20%	3.00%	0.78%	0.00%	NA
Tropical Japonica	504	34.70%	64.30%	0.99%	0.00%	NA
Japonica Intermediate	241	55.20%	43.60%	1.24%	0.00%	NA
VI/Aromatic	96	5.20%	94.80%	0.00%	0.00%	NA
Intermediate	90	75.60%	23.30%	1.11%	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
vg0703978231	A -> G	LOC_Os07g07930.1	upstream_gene_variant ; 1980.0bp to feature; MODIFIER	silent_mutation	Average:46.165; most accessible tissue: Callus, score: 78.767	N	N	N	N
vg0703978231	A -> G	LOC_Os07g07910.1	downstream_gene_variant ; 2406.0bp to feature; MODIFIER	silent_mutation	Average:46.165; most accessible tissue: Callus, score: 78.767	N	N	N	N
vg0703978231	A -> G	LOC_Os07g07920.1	downstream_gene_variant ; 514.0bp to feature; MODIFIER	silent_mutation	Average:46.165; most accessible tissue: Callus, score: 78.767	N	N	N	N
vg0703978231	A -> G	LOC_Os07g07920-LOC_Os07g07930	intergenic_region ; MODIFIER	silent_mutation	Average:46.165; most accessible tissue: Callus, score: 78.767	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0703978231	NA	7.86E-12	mr1057	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
vg0703978231	NA	7.73E-06	mr1657	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
vg0703978231	NA	7.16E-11	mr1047_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
vg0703978231	NA	8.10E-11	mr1057_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
vg0703978231	NA	7.18E-13	mr1189_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
vg0703978231	NA	3.64E-06	mr1346_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
vg0703978231	NA	3.73E-10	mr1851_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