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Detailed information for vg0706938581:

Variant ID: vg0706938581 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 6938581
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTTGTTTCAATGGCAAATCGTTGAATCGGGCAAGCTTCGTGGCATAGAGTGAATTTTCTCTAATTTTAAAGGGTCGTCACCAGCTTAACCTTTCCATCA[G/T]
TATGTATTAACTTTGGCTCAAAGACTGCATAACGTGTACAAGTGATGAGAAAATTCTATAATACTCACGTCACATTCACATATTCCCTTTAACAACCTCT

Reverse complement sequence

AGAGGTTGTTAAAGGGAATATGTGAATGTGACGTGAGTATTATAGAATTTTCTCATCACTTGTACACGTTATGCAGTCTTTGAGCCAAAGTTAATACATA[C/A]
TGATGGAAAGGTTAAGCTGGTGACGACCCTTTAAAATTAGAGAAAATTCACTCTATGCCACGAAGCTTGCCCGATTCAACGATTTGCCATTGAAACAAAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.00%	5.40%	0.72%	40.90%	NA
All Indica	2759	29.70%	1.90%	1.12%	67.23%	NA
All Japonica	1512	99.40%	0.20%	0.07%	0.33%	NA
Aus	269	9.30%	72.90%	0.74%	17.10%	NA
Indica I	595	50.90%	0.00%	0.84%	48.24%	NA
Indica II	465	18.70%	0.20%	1.08%	80.00%	NA
Indica III	913	13.90%	1.50%	1.42%	83.13%	NA
Indica Intermediate	786	38.50%	4.80%	1.02%	55.60%	NA
Temperate Japonica	767	99.70%	0.00%	0.13%	0.13%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	97.90%	1.20%	0.00%	0.83%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	67.80%	4.40%	0.00%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0706938581	G -> DEL	N	N	silent_mutation	Average:11.065; most accessible tissue: Callus, score: 54.807	N	N	N	N
vg0706938581	G -> T	LOC_Os07g12304.1	downstream_gene_variant ; 3294.0bp to feature; MODIFIER	silent_mutation	Average:11.065; most accessible tissue: Callus, score: 54.807	N	N	N	N
vg0706938581	G -> T	LOC_Os07g12310.1	intron_variant ; MODIFIER	silent_mutation	Average:11.065; most accessible tissue: Callus, score: 54.807	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0706938581	NA	1.67E-06	mr1523	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
vg0706938581	NA	2.66E-43	mr1550	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
vg0706938581	4.57E-07	2.11E-08	mr1666	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