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Detailed information for vg1001966691:

Variant ID: vg1001966691 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1966691
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGGTGTCTAGAGGGATTCCGGCAGCTTGCCGACCTTTGGCAAGGTGCTGAGAATAGTTGCCGACGAGCGTCTCCATAGGCGGCGGCCGTGCTCACGTCG[G/A]
CAGCTCAGAGGGTGGCATGATAGTGCAAAGGGATTGCTAAAATGGAATCTAGGTAGTATGTAGATTGTTGAAACGGAAGAACTCACCAAGTTATGTCGAG

Reverse complement sequence

CTCGACATAACTTGGTGAGTTCTTCCGTTTCAACAATCTACATACTACCTAGATTCCATTTTAGCAATCCCTTTGCACTATCATGCCACCCTCTGAGCTG[C/T]
CGACGTGAGCACGGCCGCCGCCTATGGAGACGCTCGTCGGCAACTATTCTCAGCACCTTGCCAAAGGTCGGCAAGCTGCCGGAATCCCTCTAGACACCTC

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	82.10%	7.90%	6.39%	3.68%	NA
All Indica	2759	86.20%	0.30%	7.76%	5.80%	NA
All Japonica	1512	75.50%	23.30%	0.93%	0.26%	NA
Aus	269	70.60%	0.40%	25.65%	3.35%	NA
Indica I	595	87.70%	0.30%	6.39%	5.55%	NA
Indica II	465	89.90%	0.20%	4.73%	5.16%	NA
Indica III	913	80.70%	0.50%	11.28%	7.45%	NA
Indica Intermediate	786	89.10%	0.00%	6.49%	4.45%	NA
Temperate Japonica	767	90.20%	8.60%	0.91%	0.26%	NA
Tropical Japonica	504	53.60%	45.40%	0.79%	0.20%	NA
Japonica Intermediate	241	74.30%	24.10%	1.24%	0.41%	NA
VI/Aromatic	96	96.90%	1.00%	2.08%	0.00%	NA
Intermediate	90	85.60%	10.00%	3.33%	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
vg1001966691	G -> A	LOC_Os10g04220.1	upstream_gene_variant ; 1622.0bp to feature; MODIFIER	silent_mutation	Average:31.058; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N
vg1001966691	G -> A	LOC_Os10g04210.1	downstream_gene_variant ; 2801.0bp to feature; MODIFIER	silent_mutation	Average:31.058; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N
vg1001966691	G -> A	LOC_Os10g04230.1	downstream_gene_variant ; 4414.0bp to feature; MODIFIER	silent_mutation	Average:31.058; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N
vg1001966691	G -> A	LOC_Os10g04210-LOC_Os10g04220	intergenic_region ; MODIFIER	silent_mutation	Average:31.058; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N
vg1001966691	G -> DEL	N	N	silent_mutation	Average:31.058; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001966691	3.30E-06	NA	mr1139	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