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Detailed information for vg0913746747:

Variant ID: vg0913746747 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 13746747
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCGAAGTTTCGCCCGATTGAGATATGGTCGCATAGCCATGATATATCGGCATAAAAATAAAGCCCGTCACGGATGACACTTACCTGTGACGGGCTATAGT[T/A]
GAGGCCCGATTGAGATGAGGGTTCCATATCTCAATCGGGCCCTAAAAGAAGCCCGTCACAGATGAGTGTCATCTGTGACGGGCTCCAACTAGAGGCCCGA

Reverse complement sequence

TCGGGCCTCTAGTTGGAGCCCGTCACAGATGACACTCATCTGTGACGGGCTTCTTTTAGGGCCCGATTGAGATATGGAACCCTCATCTCAATCGGGCCTC[A/T]
ACTATAGCCCGTCACAGGTAAGTGTCATCCGTGACGGGCTTTATTTTTATGCCGATATATCATGGCTATGCGACCATATCTCAATCGGGCGAAACTTCGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.50%	2.10%	0.36%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.04%	0.00%	NA
All Japonica	1512	92.50%	6.50%	0.99%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.10%	0.13%	0.00%	NA
Temperate Japonica	767	98.40%	1.40%	0.13%	0.00%	NA
Tropical Japonica	504	82.30%	15.70%	1.98%	0.00%	NA
Japonica Intermediate	241	94.60%	3.70%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0913746747	T -> A	LOC_Os09g23190.1	upstream_gene_variant ; 473.0bp to feature; MODIFIER	silent_mutation	Average:37.135; most accessible tissue: Zhenshan97 root, score: 55.432	N	N	N	N
vg0913746747	T -> A	LOC_Os09g23180-LOC_Os09g23190	intergenic_region ; MODIFIER	silent_mutation	Average:37.135; most accessible tissue: Zhenshan97 root, score: 55.432	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0913746747	1.10E-06	1.09E-06	mr1644	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