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Detailed information for vg0512739819:

Variant ID: vg0512739819 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 12739819
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGTATTTTCTCTTTTCTTTCTTTCTTCTTTCTTCTTTTCTTTTTTTTTTCCTTTTCTTTTCTGTTTTTTTTGGTGCGGCTTTTTTTTTTCTTTTTTTTT[G/T]
CACCTTTCTGCCTTTTTTTTTCTCACTTTTTTCTTGATTTTTTTAACAAAAACTGACTCAAGGACCTTAATGTAAGATTACAGGGACTCAAACATAAATA

Reverse complement sequence

TATTTATGTTTGAGTCCCTGTAATCTTACATTAAGGTCCTTGAGTCAGTTTTTGTTAAAAAAATCAAGAAAAAAGTGAGAAAAAAAAAGGCAGAAAGGTG[C/A]
AAAAAAAAAGAAAAAAAAAAGCCGCACCAAAAAAAACAGAAAAGAAAAGGAAAAAAAAAAGAAAAGAAGAAAGAAGAAAGAAAGAAAAGAGAAAATACTG

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	87.00%	0.30%	5.18%	7.51%	NA
All Indica	2759	87.50%	0.50%	5.04%	7.03%	NA
All Japonica	1512	96.70%	0.10%	0.53%	2.71%	NA
Aus	269	25.30%	0.00%	35.32%	39.41%	NA
Indica I	595	93.80%	0.20%	0.50%	5.55%	NA
Indica II	465	96.10%	1.50%	0.86%	1.51%	NA
Indica III	913	80.00%	0.00%	10.08%	9.97%	NA
Indica Intermediate	786	86.30%	0.60%	5.09%	8.02%	NA
Temperate Japonica	767	98.20%	0.00%	0.39%	1.43%	NA
Tropical Japonica	504	95.80%	0.20%	0.60%	3.37%	NA
Japonica Intermediate	241	93.80%	0.00%	0.83%	5.39%	NA
VI/Aromatic	96	92.70%	0.00%	0.00%	7.29%	NA
Intermediate	90	88.90%	0.00%	3.33%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0512739819	G -> T	LOC_Os05g22430.1	downstream_gene_variant ; 2749.0bp to feature; MODIFIER	silent_mutation	Average:11.542; most accessible tissue: Zhenshan97 flower, score: 19.853	N	N	N	N
vg0512739819	G -> T	LOC_Os05g22440.1	intron_variant ; MODIFIER	silent_mutation	Average:11.542; most accessible tissue: Zhenshan97 flower, score: 19.853	N	N	N	N
vg0512739819	G -> DEL	N	N	silent_mutation	Average:11.542; most accessible tissue: Zhenshan97 flower, score: 19.853	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0512739819	4.57E-06	3.64E-06	mr1974_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