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Detailed information for vg0225362516:

Variant ID: vg0225362516 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 25362516
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:

GTGAACATGTTCAGAGTCTGGTTCTTCACGTGCATGTCTCGTTCTTTTAGGGCTGTCAAATTTATTTTTAAGCATACTTGTATATAGTTACTATTTCATC[C/T]
ACCAATATGGGGCTACTATTTCGACGTAACCAACTGGAATGTGCAGACAGAGATTTCATAGCTAAGCAAGTCCACGTAGATCGAAAGCATAAGCATATTT

Reverse complement sequence

AAATATGCTTATGCTTTCGATCTACGTGGACTTGCTTAGCTATGAAATCTCTGTCTGCACATTCCAGTTGGTTACGTCGAAATAGTAGCCCCATATTGGT[G/A]
GATGAAATAGTAACTATATACAAGTATGCTTAAAAATAAATTTGACAGCCCTAAAAGAACGAGACATGCACGTGAAGAACCAGACTCTGAACATGTTCAC

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	38.10%	17.60%	1.14%	43.14%	NA
All Indica	2759	14.90%	24.70%	1.09%	59.33%	NA
All Japonica	1512	83.30%	8.00%	1.32%	7.41%	NA
Aus	269	4.10%	2.60%	0.00%	93.31%	NA
Indica I	595	6.70%	55.50%	1.68%	36.13%	NA
Indica II	465	4.10%	24.70%	1.51%	69.68%	NA
Indica III	913	28.50%	6.80%	0.33%	64.40%	NA
Indica Intermediate	786	11.70%	22.10%	1.27%	64.89%	NA
Temperate Japonica	767	94.80%	2.20%	1.56%	1.43%	NA
Tropical Japonica	504	71.60%	14.50%	0.79%	13.10%	NA
Japonica Intermediate	241	71.00%	12.90%	1.66%	14.52%	NA
VI/Aromatic	96	71.90%	15.60%	1.04%	11.46%	NA
Intermediate	90	54.40%	11.10%	3.33%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0225362516	C -> T	LOC_Os02g42160.1	upstream_gene_variant ; 2505.0bp to feature; MODIFIER	silent_mutation	Average:69.163; most accessible tissue: Callus, score: 94.343	N	N	N	N
vg0225362516	C -> T	LOC_Os02g42170.1	upstream_gene_variant ; 2118.0bp to feature; MODIFIER	silent_mutation	Average:69.163; most accessible tissue: Callus, score: 94.343	N	N	N	N
vg0225362516	C -> T	LOC_Os02g42180.1	upstream_gene_variant ; 4424.0bp to feature; MODIFIER	silent_mutation	Average:69.163; most accessible tissue: Callus, score: 94.343	N	N	N	N
vg0225362516	C -> T	LOC_Os02g42160-LOC_Os02g42170	intergenic_region ; MODIFIER	silent_mutation	Average:69.163; most accessible tissue: Callus, score: 94.343	N	N	N	N
vg0225362516	C -> DEL	N	N	silent_mutation	Average:69.163; most accessible tissue: Callus, score: 94.343	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0225362516	NA	3.22E-10	mr1175	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
vg0225362516	NA	8.86E-08	mr1403	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