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Detailed information for vg1212739494:

Variant ID: vg1212739494 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 12739494
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.83, A: 0.16, others allele: 0.00, population size: 159. )

Flanking Sequence (100 bp) in Reference Genome:

CAACCACCGTACTCAGCAAGTCACACCGGGAGATGCATGATTAATGCAAGGGGGTACAAGGAGTAATAATATAGGGGTTAAGTTTCGCAGTAAACAGCAT[T/A]
TAAAAGTCACTTAGTTGCCCAAAGCTATTTTATAAAGACGATCCTAGAGCTACACAGTATTATTAATCAAGGCCGTGGACCCACACGAACCTGCCTTAAC

Reverse complement sequence

GTTAAGGCAGGTTCGTGTGGGTCCACGGCCTTGATTAATAATACTGTGTAGCTCTAGGATCGTCTTTATAAAATAGCTTTGGGCAACTAAGTGACTTTTA[A/T]
ATGCTGTTTACTGCGAAACTTAACCCCTATATTATTACTCCTTGTACCCCCTTGCATTAATCATGCATCTCCCGGTGTGACTTGCTGAGTACGGTGGTTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.60%	16.40%	0.00%	0.00%	NA
All Indica	2759	96.60%	3.40%	0.00%	0.00%	NA
All Japonica	1512	56.90%	43.10%	0.00%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	99.30%	0.70%	0.00%	0.00%	NA
Indica II	465	97.00%	3.00%	0.00%	0.00%	NA
Indica III	913	96.70%	3.30%	0.00%	0.00%	NA
Indica Intermediate	786	94.30%	5.70%	0.00%	0.00%	NA
Temperate Japonica	767	23.30%	76.70%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	1.40%	0.00%	0.00%	NA
Japonica Intermediate	241	76.80%	23.20%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	71.10%	28.90%	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
vg1212739494	T -> A	LOC_Os12g22550.1	downstream_gene_variant ; 4561.0bp to feature; MODIFIER	silent_mutation	Average:31.441; most accessible tissue: Zhenshan97 root, score: 49.075	N	N	N	N
vg1212739494	T -> A	LOC_Os12g22560.1	downstream_gene_variant ; 2828.0bp to feature; MODIFIER	silent_mutation	Average:31.441; most accessible tissue: Zhenshan97 root, score: 49.075	N	N	N	N
vg1212739494	T -> A	LOC_Os12g22580.1	downstream_gene_variant ; 4197.0bp to feature; MODIFIER	silent_mutation	Average:31.441; most accessible tissue: Zhenshan97 root, score: 49.075	N	N	N	N
vg1212739494	T -> A	LOC_Os12g22570.1	intron_variant ; MODIFIER	silent_mutation	Average:31.441; most accessible tissue: Zhenshan97 root, score: 49.075	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1212739494	NA	4.75E-15	mr1023	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
vg1212739494	NA	6.35E-10	mr1178	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
vg1212739494	NA	8.12E-07	mr1334	Ind_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
vg1212739494	3.36E-06	2.12E-07	mr1363	Ind_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
vg1212739494	NA	3.04E-09	mr1368	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
vg1212739494	NA	3.72E-14	mr1489	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
vg1212739494	NA	3.63E-14	mr1491	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
vg1212739494	NA	7.65E-09	mr1606	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
vg1212739494	NA	2.32E-06	mr1606	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
vg1212739494	NA	6.39E-06	mr1657	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
vg1212739494	NA	2.18E-08	mr1338_2	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