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Detailed information for vg0907671668:

Variant ID: vg0907671668 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7671668
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAGGAAGGCAACTTCTGGTGCATGCTTCTGACACCACTGCCAACTTAACCTACACACAAGATAAACGATCTTATAAGCAAGTTAAACCGATTGTTATTA[C/A]
CAGATTGAGTTGGGCGACAATACTTACAAGCAGTAGCACTTAAGGAGGCTTGTGTCCACCGCTCGGAGCCTGTAGAGGTCGAAAAGATCCTTGAAGTTGA

Reverse complement sequence

TCAACTTCAAGGATCTTTTCGACCTCTACAGGCTCCGAGCGGTGGACACAAGCCTCCTTAAGTGCTACTGCTTGTAAGTATTGTCGCCCAACTCAATCTG[G/T]
TAATAACAATCGGTTTAACTTGCTTATAAGATCGTTTATCTTGTGTGTAGGTTAAGTTGGCAGTGGTGTCAGAAGCATGCACCAGAAGTTGCCTTCCTTG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	35.60%	8.60%	1.08%	54.72%	NA
All Indica	2759	18.30%	1.80%	1.59%	78.29%	NA
All Japonica	1512	64.80%	22.90%	0.20%	12.04%	NA
Aus	269	19.00%	0.00%	1.49%	79.55%	NA
Indica I	595	16.60%	2.50%	2.02%	78.82%	NA
Indica II	465	10.50%	1.10%	1.29%	87.10%	NA
Indica III	913	23.20%	1.00%	1.10%	74.70%	NA
Indica Intermediate	786	18.60%	2.50%	2.04%	76.84%	NA
Temperate Japonica	767	65.60%	12.80%	0.39%	21.25%	NA
Tropical Japonica	504	75.60%	23.00%	0.00%	1.39%	NA
Japonica Intermediate	241	39.80%	55.20%	0.00%	4.98%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	60.00%	11.10%	0.00%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0907671668	C -> DEL	N	N	silent_mutation	Average:6.314; most accessible tissue: Callus, score: 17.238	N	N	N	N
vg0907671668	C -> A	LOC_Os09g13310.1	upstream_gene_variant ; 4195.0bp to feature; MODIFIER	silent_mutation	Average:6.314; most accessible tissue: Callus, score: 17.238	N	N	N	N
vg0907671668	C -> A	LOC_Os09g13300.1	intron_variant ; MODIFIER	silent_mutation	Average:6.314; most accessible tissue: Callus, score: 17.238	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907671668	3.90E-06	NA	mr1002	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
vg0907671668	2.34E-06	NA	mr1263	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
vg0907671668	2.34E-06	NA	mr1451	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
vg0907671668	NA	8.11E-06	mr1633_2	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