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Detailed information for vg0901718260:

Variant ID: vg0901718260 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 1718260
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, C: 0.07, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

GACACTATCGGTTTTCCCAGTCACAAACAAGCTGTTCTAATCTAGTATAATGTACCAGCTTGGGACACTGGTATCATGTGTTGCTCTTTTATATACTGGC[T/C]
ATTAAATTCCCCGGGCTTCAACCTCCTTGTTTCTACATGCCACTACTTTTTTTGCTACAATGTAAGCCATGCAAGTTTGTGATAGAGAAAAGTAATGTAG

Reverse complement sequence

CTACATTACTTTTCTCTATCACAAACTTGCATGGCTTACATTGTAGCAAAAAAAGTAGTGGCATGTAGAAACAAGGAGGTTGAAGCCCGGGGAATTTAAT[A/G]
GCCAGTATATAAAAGAGCAACACATGATACCAGTGTCCCAAGCTGGTACATTATACTAGATTAGAACAGCTTGTTTGTGACTGGGAAAACCGATAGTGTC

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	61.80%	33.40%	0.08%	4.74%	NA
All Indica	2759	93.60%	6.30%	0.04%	0.04%	NA
All Japonica	1512	1.50%	83.70%	0.20%	14.62%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	94.10%	5.90%	0.00%	0.00%	NA
Indica II	465	92.00%	8.00%	0.00%	0.00%	NA
Indica III	913	96.70%	3.20%	0.00%	0.11%	NA
Indica Intermediate	786	90.50%	9.40%	0.13%	0.00%	NA
Temperate Japonica	767	1.20%	85.70%	0.26%	12.91%	NA
Tropical Japonica	504	1.40%	81.00%	0.00%	17.66%	NA
Japonica Intermediate	241	2.50%	83.40%	0.41%	13.69%	NA
VI/Aromatic	96	8.30%	91.70%	0.00%	0.00%	NA
Intermediate	90	46.70%	51.10%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0901718260	T -> DEL	N	N	silent_mutation	Average:70.486; most accessible tissue: Callus, score: 89.113	N	N	N	N
vg0901718260	T -> C	LOC_Os09g03480.1	upstream_gene_variant ; 2121.0bp to feature; MODIFIER	silent_mutation	Average:70.486; most accessible tissue: Callus, score: 89.113	N	N	N	N
vg0901718260	T -> C	LOC_Os09g03490.1	upstream_gene_variant ; 3131.0bp to feature; MODIFIER	silent_mutation	Average:70.486; most accessible tissue: Callus, score: 89.113	N	N	N	N
vg0901718260	T -> C	LOC_Os09g03480-LOC_Os09g03490	intergenic_region ; MODIFIER	silent_mutation	Average:70.486; most accessible tissue: Callus, score: 89.113	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0901718260	2.93E-06	2.93E-06	mr1122	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
vg0901718260	2.11E-06	NA	mr1705_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