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Detailed information for vg0222144498:

Variant ID: vg0222144498 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22144498
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

TTTCATAAAAGTGCAACAAAGGTAATCTGTAAAAAAAAAAAATCACAAGTGACTGACAAACACATACAGCACAATTTGGTGTCAACCAACCACCACCGAT[T/G]
GAAACTCCTTTTAGTAAAAAAAAAAACATGGCACGAGTTTGAGCAATGGTGCAAGAGCAAAGATTGGGATTCAGTTTGCATCGCTGAATGAATCGCCAAC

Reverse complement sequence

GTTGGCGATTCATTCAGCGATGCAAACTGAATCCCAATCTTTGCTCTTGCACCATTGCTCAAACTCGTGCCATGTTTTTTTTTTTACTAAAAGGAGTTTC[A/C]
ATCGGTGGTGGTTGGTTGACACCAAATTGTGCTGTATGTGTTTGTCAGTCACTTGTGATTTTTTTTTTTTACAGATTACCTTTGTTGCACTTTTATGAAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.10%	8.70%	0.21%	0.00%	NA
All Indica	2759	95.70%	4.20%	0.07%	0.00%	NA
All Japonica	1512	84.40%	15.10%	0.53%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.80%	1.00%	0.17%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	93.20%	6.70%	0.11%	0.00%	NA
Indica Intermediate	786	93.80%	6.20%	0.00%	0.00%	NA
Temperate Japonica	767	91.00%	8.70%	0.26%	0.00%	NA
Tropical Japonica	504	90.10%	9.70%	0.20%	0.00%	NA
Japonica Intermediate	241	51.50%	46.50%	2.07%	0.00%	NA
VI/Aromatic	96	40.60%	59.40%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg0222144498	T -> G	LOC_Os02g36680.1	upstream_gene_variant ; 2502.0bp to feature; MODIFIER	silent_mutation	Average:43.509; most accessible tissue: Callus, score: 74.466	N	N	N	N
vg0222144498	T -> G	LOC_Os02g36700.1	downstream_gene_variant ; 1922.0bp to feature; MODIFIER	silent_mutation	Average:43.509; most accessible tissue: Callus, score: 74.466	N	N	N	N
vg0222144498	T -> G	LOC_Os02g36690.1	intron_variant ; MODIFIER	silent_mutation	Average:43.509; most accessible tissue: Callus, score: 74.466	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222144498	NA	2.40E-06	mr1057	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
vg0222144498	NA	6.55E-06	mr1913	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
vg0222144498	NA	6.59E-07	mr1057_2	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
vg0222144498	NA	4.32E-06	mr1113_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
vg0222144498	NA	1.81E-06	mr1118_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
vg0222144498	NA	8.75E-06	mr1123_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
vg0222144498	NA	4.04E-06	mr1240_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
vg0222144498	8.35E-08	NA	mr1334_2	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
vg0222144498	NA	9.65E-07	mr1496_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
vg0222144498	NA	4.76E-07	mr1691_2	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
vg0222144498	1.47E-06	NA	mr1991_2	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