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Detailed information for vg0714342439:

Variant ID: vg0714342439 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14342439
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGAGTTACCGCACGGAAAATTTGATTTTTCCGTGCCGTCCTCTTTAATGGACCACACGCGAAAATGAGCCGATTTTCCCAGAAGCAACGAGATACCGCCC[T/G]
CACGGAATCTAAAAGGTCCCTATCCAGGAAAATCGTTTCTATAGTAGTGATTCATGAAGTTCCTTCTCTACTTGATCGATCCATTTTCTTTGTTTCTTTT

Reverse complement sequence

AAAAGAAACAAAGAAAATGGATCGATCAAGTAGAGAAGGAACTTCATGAATCACTACTATAGAAACGATTTTCCTGGATAGGGACCTTTTAGATTCCGTG[A/C]
GGGCGGTATCTCGTTGCTTCTGGGAAAATCGGCTCATTTTCGCGTGTGGTCCATTAAAGAGGACGGCACGGAAAAATCAAATTTTCCGTGCGGTAACTCG

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	50.60%	40.30%	3.83%	5.27%	NA
All Indica	2759	76.10%	17.50%	5.29%	1.16%	NA
All Japonica	1512	1.80%	83.00%	1.32%	13.89%	NA
Aus	269	81.00%	14.10%	4.09%	0.74%	NA
Indica I	595	54.10%	36.10%	7.73%	2.02%	NA
Indica II	465	72.30%	21.90%	5.38%	0.43%	NA
Indica III	913	97.50%	1.90%	0.55%	0.11%	NA
Indica Intermediate	786	70.10%	18.80%	8.91%	2.16%	NA
Temperate Japonica	767	1.60%	85.30%	1.30%	11.86%	NA
Tropical Japonica	504	0.60%	92.10%	1.39%	5.95%	NA
Japonica Intermediate	241	5.00%	56.80%	1.24%	36.93%	NA
VI/Aromatic	96	15.60%	80.20%	0.00%	4.17%	NA
Intermediate	90	37.80%	56.70%	4.44%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714342439	T -> DEL	N	N	silent_mutation	Average:18.085; most accessible tissue: Callus, score: 51.31	N	N	N	N
vg0714342439	T -> G	LOC_Os07g25100.1	upstream_gene_variant ; 3823.0bp to feature; MODIFIER	silent_mutation	Average:18.085; most accessible tissue: Callus, score: 51.31	N	N	N	N
vg0714342439	T -> G	LOC_Os07g25110.1	downstream_gene_variant ; 1082.0bp to feature; MODIFIER	silent_mutation	Average:18.085; most accessible tissue: Callus, score: 51.31	N	N	N	N
vg0714342439	T -> G	LOC_Os07g25100-LOC_Os07g25110	intergenic_region ; MODIFIER	silent_mutation	Average:18.085; most accessible tissue: Callus, score: 51.31	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714342439	2.57E-06	2.57E-06	mr1375	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