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Detailed information for vg0617787176:

Variant ID: vg0617787176 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 17787176
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAAATTTAAGTAATTATTAATTCTTTTCGAATCATTTGATTTATTGTTAAATATACGTTTATGTATACATATAGTTTTACACATTTTACAAAAGTTTTT[G/T]
AATAAGACGAACGGTCAAATATATTTAAAAAAGTCAACGGCGTCAAACATTTATAGAAGGAGGGAGTATGTGTGTCTAGATTCATTATCATCTATATGAA

Reverse complement sequence

TTCATATAGATGATAATGAATCTAGACACACATACTCCCTCCTTCTATAAATGTTTGACGCCGTTGACTTTTTTAAATATATTTGACCGTTCGTCTTATT[C/A]
AAAAACTTTTGTAAAATGTGTAAAACTATATGTATACATAAACGTATATTTAACAATAAATCAAATGATTCGAAAAGAATTAATAATTACTTAAATTTTT

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	92.00%	7.10%	0.17%	0.68%	NA
All Indica	2759	87.70%	10.80%	0.29%	1.16%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	90.00%	10.00%	0.00%	0.00%	NA
Indica I	595	87.10%	11.60%	0.34%	1.01%	NA
Indica II	465	97.60%	1.50%	0.65%	0.22%	NA
Indica III	913	84.60%	13.90%	0.00%	1.53%	NA
Indica Intermediate	786	86.00%	12.20%	0.38%	1.40%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	0.00%	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
vg0617787176	G -> T	LOC_Os06g30680-LOC_Os06g30690	intergenic_region ; MODIFIER	silent_mutation	Average:38.333; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0617787176	G -> DEL	N	N	silent_mutation	Average:38.333; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0617787176	NA	2.62E-06	mr1706	Ind_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
vg0617787176	5.87E-06	2.24E-06	mr1064_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
vg0617787176	NA	9.33E-07	mr1268_2	Ind_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
vg0617787176	NA	2.65E-08	mr1327_2	Ind_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