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Detailed information for vg0212125821:

Variant ID: vg0212125821 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 12125821
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:

TCTCCATAAGTGGTAACCAGGGTCAATAGTCTGAACTTGGCCGGGGAGAGGACGTTAAGATGAATCAAACAATATCAGTTTCAATCAATTTGTGACCAGA[C/T]
AATGGAGCTTATCATACAACAGACGCAGCACACGTACATGTTGTGTGGTTTGCAGGCCTAGTTCTAGTGCACAACTGCTGACCAAAAAAGTTCATGAACA

Reverse complement sequence

TGTTCATGAACTTTTTTGGTCAGCAGTTGTGCACTAGAACTAGGCCTGCAAACCACACAACATGTACGTGTGCTGCGTCTGTTGTATGATAAGCTCCATT[G/A]
TCTGGTCACAAATTGATTGAAACTGATATTGTTTGATTCATCTTAACGTCCTCTCCCCGGCCAAGTTCAGACTATTGACCCTGGTTACCACTTATGGAGA

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	98.70%	0.80%	0.47%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.04%	0.00%	NA
All Japonica	1512	96.20%	2.40%	1.39%	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	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	93.10%	4.20%	2.74%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	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
vg0212125821	C -> T	LOC_Os02g20550.1	downstream_gene_variant ; 1943.0bp to feature; MODIFIER	silent_mutation	Average:60.601; most accessible tissue: Zhenshan97 young leaf, score: 81.841	N	N	N	N
vg0212125821	C -> T	LOC_Os02g20560.1	downstream_gene_variant ; 2091.0bp to feature; MODIFIER	silent_mutation	Average:60.601; most accessible tissue: Zhenshan97 young leaf, score: 81.841	N	N	N	N
vg0212125821	C -> T	LOC_Os02g20550-LOC_Os02g20560	intergenic_region ; MODIFIER	silent_mutation	Average:60.601; most accessible tissue: Zhenshan97 young leaf, score: 81.841	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0212125821	1.38E-06	NA	mr1446	Jap_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
vg0212125821	5.91E-07	4.19E-07	mr1989	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