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Detailed information for vg0910447508:

Variant ID: vg0910447508 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10447508
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATAAGAGGTAGCAAAACTGAACTTGGCTAGCTGCTTGGAGGTAAATAAGAGGATGCAAGGAAAGGATTGTTCGATTAATGAATCGTCTAGCTCTAGTCT[C/T]
AGTTCGTGCCACTTTTTTTCCCCAAAAATTCTTGATTGTTTAGAAATATTTGATGCTTAAGTGAGAGACCTGTGAACGTTAGGATTCAATTATTTTGTGA

Reverse complement sequence

TCACAAAATAATTGAATCCTAACGTTCACAGGTCTCTCACTTAAGCATCAAATATTTCTAAACAATCAAGAATTTTTGGGGAAAAAAAGTGGCACGAACT[G/A]
AGACTAGAGCTAGACGATTCATTAATCGAACAATCCTTTCCTTGCATCCTCTTATTTACCTCCAAGCAGCTAGCCAAGTTCAGTTTTGCTACCTCTTATC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	40.50%	4.40%	0.40%	54.68%	NA
All Indica	2759	9.50%	0.20%	0.33%	90.00%	NA
All Japonica	1512	85.10%	12.00%	0.66%	2.25%	NA
Aus	269	79.90%	6.70%	0.00%	13.38%	NA
Indica I	595	16.60%	0.00%	0.00%	83.36%	NA
Indica II	465	10.30%	0.00%	0.43%	89.25%	NA
Indica III	913	3.90%	0.00%	0.22%	95.84%	NA
Indica Intermediate	786	10.10%	0.60%	0.64%	88.68%	NA
Temperate Japonica	767	81.10%	16.60%	1.30%	1.04%	NA
Tropical Japonica	504	95.40%	2.00%	0.00%	2.58%	NA
Japonica Intermediate	241	75.90%	18.70%	0.00%	5.39%	NA
VI/Aromatic	96	93.80%	0.00%	0.00%	6.25%	NA
Intermediate	90	68.90%	3.30%	0.00%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0910447508	C -> DEL	N	N	silent_mutation	Average:14.939; most accessible tissue: Callus, score: 97.298	N	N	N	N
vg0910447508	C -> T	LOC_Os09g17049.1	upstream_gene_variant ; 906.0bp to feature; MODIFIER	silent_mutation	Average:14.939; most accessible tissue: Callus, score: 97.298	N	N	N	N
vg0910447508	C -> T	LOC_Os09g17049.2	upstream_gene_variant ; 3417.0bp to feature; MODIFIER	silent_mutation	Average:14.939; most accessible tissue: Callus, score: 97.298	N	N	N	N
vg0910447508	C -> T	LOC_Os09g17040.1	intron_variant ; MODIFIER	silent_mutation	Average:14.939; most accessible tissue: Callus, score: 97.298	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910447508	7.88E-06	NA	mr1507	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
vg0910447508	8.00E-06	NA	mr1579	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
vg0910447508	8.14E-06	NA	mr1680	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
vg0910447508	2.19E-06	6.08E-06	mr1809	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