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Detailed information for vg0910442886:

Variant ID: vg0910442886 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10442886
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATGAAAAGGATTCAGAGGGCTCTTAGGTTTTTCCATTCGGCTTGTCCTACGGTCAACCTGGCTCTGATACCAACTTGTCACACCCAGAAATTCCCGAAT[A/G]
GAATTCCAAGCAGAATGTGTATTAAAACCCCCGTCCAGGACCAGCCGGGGTACACAAACGACAATGTTGACATACAGATCCTCGTCTTACAAACATTATA

Reverse complement sequence

TATAATGTTTGTAAGACGAGGATCTGTATGTCAACATTGTCGTTTGTGTACCCCGGCTGGTCCTGGACGGGGGTTTTAATACACATTCTGCTTGGAATTC[T/C]
ATTCGGGAATTTCTGGGTGTGACAAGTTGGTATCAGAGCCAGGTTGACCGTAGGACAAGCCGAATGGAAAAACCTAAGAGCCCTCTGAATCCTTTTCATT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.30%	0.40%	1.18%	5.14%	NA
All Indica	2759	98.30%	0.70%	0.94%	0.14%	NA
All Japonica	1512	87.00%	0.10%	1.65%	11.24%	NA
Aus	269	75.80%	0.00%	1.49%	22.68%	NA
Indica I	595	99.50%	0.20%	0.17%	0.17%	NA
Indica II	465	98.30%	0.90%	0.86%	0.00%	NA
Indica III	913	97.90%	0.80%	1.31%	0.00%	NA
Indica Intermediate	786	97.70%	0.80%	1.15%	0.38%	NA
Temperate Japonica	767	87.90%	0.00%	1.69%	10.43%	NA
Tropical Japonica	504	86.50%	0.20%	1.39%	11.90%	NA
Japonica Intermediate	241	85.50%	0.00%	2.07%	12.45%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	94.40%	0.00%	1.11%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0910442886	A -> G	LOC_Os09g17030.1	upstream_gene_variant ; 519.0bp to feature; MODIFIER	silent_mutation	Average:16.577; most accessible tissue: Zhenshan97 flag leaf, score: 36.135	N	N	N	N
vg0910442886	A -> G	LOC_Os09g17040.1	downstream_gene_variant ; 3836.0bp to feature; MODIFIER	silent_mutation	Average:16.577; most accessible tissue: Zhenshan97 flag leaf, score: 36.135	N	N	N	N
vg0910442886	A -> G	LOC_Os09g17030-LOC_Os09g17040	intergenic_region ; MODIFIER	silent_mutation	Average:16.577; most accessible tissue: Zhenshan97 flag leaf, score: 36.135	N	N	N	N
vg0910442886	A -> DEL	N	N	silent_mutation	Average:16.577; most accessible tissue: Zhenshan97 flag leaf, score: 36.135	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910442886	3.80E-06	NA	mr1976_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