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Detailed information for vg1008204929:

Variant ID: vg1008204929 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 8204929
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTCTTTCGACGTATGCGGTTGTCATTTCGACAACAGCTAGCGCCGACCGTTGGGACCTCCGAGCGAAACCACTGAGAGCGAATGCCACCGAAGAGGGTC[G/A]
TGAAGGAGAAGGTTGCCAGGCGGAGGGAGAGCGACGCCGGACTGGACATGGCTGCCGAGGAAGGAGCAGAGCCTTCGGCGCCCGTGGCCGAAGATGGAGG

Reverse complement sequence

CCTCCATCTTCGGCCACGGGCGCCGAAGGCTCTGCTCCTTCCTCGGCAGCCATGTCCAGTCCGGCGTCGCTCTCCCTCCGCCTGGCAACCTTCTCCTTCA[C/T]
GACCCTCTTCGGTGGCATTCGCTCTCAGTGGTTTCGCTCGGAGGTCCCAACGGTCGGCGCTAGCTGTTGTCGAAATGACAACCGCATACGTCGAAAGACG

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	89.10%	9.20%	0.30%	1.48%	NA
All Indica	2759	99.10%	0.80%	0.07%	0.04%	NA
All Japonica	1512	71.00%	23.90%	0.60%	4.50%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.20%	0.22%	0.00%	NA
Indica III	913	97.90%	2.00%	0.11%	0.00%	NA
Indica Intermediate	786	99.50%	0.40%	0.00%	0.13%	NA
Temperate Japonica	767	71.60%	18.60%	1.04%	8.74%	NA
Tropical Japonica	504	61.10%	38.70%	0.20%	0.00%	NA
Japonica Intermediate	241	90.00%	9.50%	0.00%	0.41%	NA
VI/Aromatic	96	60.40%	39.60%	0.00%	0.00%	NA
Intermediate	90	82.20%	13.30%	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
vg1008204929	G -> A	LOC_Os10g16450.1	upstream_gene_variant ; 342.0bp to feature; MODIFIER	silent_mutation	Average:70.296; most accessible tissue: Zhenshan97 flag leaf, score: 82.529	N	N	N	N
vg1008204929	G -> A	LOC_Os10g16460.1	upstream_gene_variant ; 2102.0bp to feature; MODIFIER	silent_mutation	Average:70.296; most accessible tissue: Zhenshan97 flag leaf, score: 82.529	N	N	N	N
vg1008204929	G -> A	LOC_Os10g16440.1	downstream_gene_variant ; 3857.0bp to feature; MODIFIER	silent_mutation	Average:70.296; most accessible tissue: Zhenshan97 flag leaf, score: 82.529	N	N	N	N
vg1008204929	G -> A	LOC_Os10g16440.2	downstream_gene_variant ; 3857.0bp to feature; MODIFIER	silent_mutation	Average:70.296; most accessible tissue: Zhenshan97 flag leaf, score: 82.529	N	N	N	N
vg1008204929	G -> A	LOC_Os10g16440-LOC_Os10g16450	intergenic_region ; MODIFIER	silent_mutation	Average:70.296; most accessible tissue: Zhenshan97 flag leaf, score: 82.529	N	N	N	N
vg1008204929	G -> DEL	N	N	silent_mutation	Average:70.296; most accessible tissue: Zhenshan97 flag leaf, score: 82.529	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1008204929	NA	5.43E-07	mr1398_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