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Detailed information for vg1012629654:

Variant ID: vg1012629654 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 12629654
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATATAAAATAAACAAACATGTAGAACATGATTTTAGATGAATTATGAGACTTGAACGGCCCTATTCTGACTTCAAATGAATTTAATATGAATTTTACAA[G/A]
ATTAAATCTAATTAAAGCCCATTAAAAAGAATTAAATAAATTTAATTCAATTTATGGACAATTTTAATATGTAGATCTTTATTTTAGAAAAATTTAGCAA

Reverse complement sequence

TTGCTAAATTTTTCTAAAATAAAGATCTACATATTAAAATTGTCCATAAATTGAATTAAATTTATTTAATTCTTTTTAATGGGCTTTAATTAGATTTAAT[C/T]
TTGTAAAATTCATATTAAATTCATTTGAAGTCAGAATAGGGCCGTTCAAGTCTCATAATTCATCTAAAATCATGTTCTACATGTTTGTTTATTTTATATG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.50%	0.10%	2.37%	23.00%	NA
All Indica	2759	64.20%	0.00%	2.46%	33.31%	NA
All Japonica	1512	88.60%	0.30%	1.12%	10.05%	NA
Aus	269	94.40%	0.00%	5.58%	0.00%	NA
Indica I	595	53.90%	0.00%	2.18%	43.87%	NA
Indica II	465	62.60%	0.00%	2.15%	35.27%	NA
Indica III	913	69.90%	0.00%	2.96%	27.16%	NA
Indica Intermediate	786	66.40%	0.00%	2.29%	31.30%	NA
Temperate Japonica	767	96.10%	0.10%	0.00%	3.78%	NA
Tropical Japonica	504	77.60%	0.40%	2.78%	19.25%	NA
Japonica Intermediate	241	87.60%	0.40%	1.24%	10.79%	NA
VI/Aromatic	96	86.50%	0.00%	12.50%	1.04%	NA
Intermediate	90	83.30%	0.00%	0.00%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1012629654	G -> A	LOC_Os10g24620.1	upstream_gene_variant ; 4340.0bp to feature; MODIFIER	silent_mutation	Average:13.788; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1012629654	G -> A	LOC_Os10g24600.1	downstream_gene_variant ; 2603.0bp to feature; MODIFIER	silent_mutation	Average:13.788; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1012629654	G -> A	LOC_Os10g24610.1	downstream_gene_variant ; 1159.0bp to feature; MODIFIER	silent_mutation	Average:13.788; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1012629654	G -> A	LOC_Os10g24610-LOC_Os10g24620	intergenic_region ; MODIFIER	silent_mutation	Average:13.788; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1012629654	G -> DEL	N	N	silent_mutation	Average:13.788; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1012629654	1.76E-06	5.52E-06	mr1748_2	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