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Detailed information for vg1008646727:

Variant ID: vg1008646727 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 8646727
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTGTACCCCGGCTTTTCCTGGGACGGGGATTAATACACTAGCGTTCGGGAAAAGGCAATTTTCCCGGTCGCGACAAGGTGGTATCAGAGCCATCTCGAT[T/A]
GTAGGATAAGCCAAGTGGATAAAACCTAAGGACATATTTTATAAATAAAACTATTTGCGAAAGTTCCTCTTTTTCTCCTTCCCCTAATGCTATTTGCAAA

Reverse complement sequence

TTTGCAAATAGCATTAGGGGAAGGAGAAAAAGAGGAACTTTCGCAAATAGTTTTATTTATAAAATATGTCCTTAGGTTTTATCCACTTGGCTTATCCTAC[A/T]
ATCGAGATGGCTCTGATACCACCTTGTCGCGACCGGGAAAATTGCCTTTTCCCGAACGCTAGTGTATTAATCCCCGTCCCAGGAAAAGCCGGGGTACACC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	15.10%	0.30%	7.98%	76.68%	NA
All Indica	2759	2.80%	0.30%	8.37%	88.55%	NA
All Japonica	1512	40.30%	0.00%	1.98%	57.67%	NA
Aus	269	3.00%	1.50%	32.71%	62.83%	NA
Indica I	595	2.40%	0.50%	1.34%	95.80%	NA
Indica II	465	1.70%	0.40%	3.01%	94.84%	NA
Indica III	913	3.20%	0.10%	17.20%	79.52%	NA
Indica Intermediate	786	3.20%	0.40%	6.62%	89.82%	NA
Temperate Japonica	767	55.00%	0.00%	1.96%	43.02%	NA
Tropical Japonica	504	10.90%	0.00%	2.58%	86.51%	NA
Japonica Intermediate	241	55.20%	0.00%	0.83%	43.98%	NA
VI/Aromatic	96	1.00%	0.00%	20.83%	78.12%	NA
Intermediate	90	18.90%	0.00%	8.89%	72.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1008646727	T -> A	LOC_Os10g17210.1	upstream_gene_variant ; 643.0bp to feature; MODIFIER	silent_mutation	Average:8.449; most accessible tissue: Zhenshan97 root, score: 15.132	N	N	N	N
vg1008646727	T -> A	LOC_Os10g17180-LOC_Os10g17210	intergenic_region ; MODIFIER	silent_mutation	Average:8.449; most accessible tissue: Zhenshan97 root, score: 15.132	N	N	N	N
vg1008646727	T -> DEL	N	N	silent_mutation	Average:8.449; most accessible tissue: Zhenshan97 root, score: 15.132	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1008646727	2.55E-06	8.63E-07	mr1011	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