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Detailed information for vg1011003845:

Variant ID: vg1011003845 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 11003845
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCCGCCATCGAATTCCACACGCTCTACTACCACATCAAGGTGACGCGCACACCCTCTACGTGTATGCTTCTTGTTTGTGTTGTGGCGTGGGGATTGGCC[G/A]
TGATGCCATTGTTGTTGTTGTTGCTTGTGTGTGCAGACAACGAAGAGGGTCAGGTGGATAAGGCGCGAGGTGCACAGGCGTCATGGCGGAGGCAGGTGAG

Reverse complement sequence

CTCACCTGCCTCCGCCATGACGCCTGTGCACCTCGCGCCTTATCCACCTGACCCTCTTCGTTGTCTGCACACACAAGCAACAACAACAACAATGGCATCA[C/T]
GGCCAATCCCCACGCCACAACACAAACAAGAAGCATACACGTAGAGGGTGTGCGCGTCACCTTGATGTGGTAGTAGAGCGTGTGGAATTCGATGGCGGAG

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	86.10%	3.10%	1.80%	8.99%	NA
All Indica	2759	97.90%	0.40%	0.25%	1.49%	NA
All Japonica	1512	62.70%	8.30%	4.89%	24.14%	NA
Aus	269	97.80%	0.00%	0.74%	1.49%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	95.20%	0.50%	0.77%	3.50%	NA
Indica Intermediate	786	98.10%	0.80%	0.00%	1.15%	NA
Temperate Japonica	767	92.00%	0.80%	0.13%	7.04%	NA
Tropical Japonica	504	17.70%	20.80%	12.30%	49.21%	NA
Japonica Intermediate	241	63.50%	5.80%	4.56%	26.14%	NA
VI/Aromatic	96	89.60%	3.10%	1.04%	6.25%	NA
Intermediate	90	82.20%	6.70%	1.11%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1011003845	G -> A	LOC_Os10g21479.1	upstream_gene_variant ; 333.0bp to feature; MODIFIER	silent_mutation	Average:75.826; most accessible tissue: Zhenshan97 young leaf, score: 91.616	N	N	N	N
vg1011003845	G -> A	LOC_Os10g21490.1	downstream_gene_variant ; 3411.0bp to feature; MODIFIER	silent_mutation	Average:75.826; most accessible tissue: Zhenshan97 young leaf, score: 91.616	N	N	N	N
vg1011003845	G -> A	LOC_Os10g21479-LOC_Os10g21490	intergenic_region ; MODIFIER	silent_mutation	Average:75.826; most accessible tissue: Zhenshan97 young leaf, score: 91.616	N	N	N	N
vg1011003845	G -> DEL	N	N	silent_mutation	Average:75.826; most accessible tissue: Zhenshan97 young leaf, score: 91.616	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1011003845	NA	4.75E-07	mr1633_2	Jap_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
vg1011003845	5.42E-06	NA	mr1894_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