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Detailed information for vg0226608386:

Variant ID: vg0226608386 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 26608386
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, T: 0.11, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:

AGATAGATAGATAGATAGATAGATATAATAGATAGATAGATAGATAGATAGATTATCTTAGCCAGAAAAGGGACATGGCTTCCAAATTTCCTGGTACAAA[C/T]
CAAATCTAATGCAAATTGATCTTATCAATTGTGTCGATGAAATTTTACAATTTTGATTTCCCCTTCCAGACAACAATCGCAGAAAGTGACCTTTTACATG

Reverse complement sequence

CATGTAAAAGGTCACTTTCTGCGATTGTTGTCTGGAAGGGGAAATCAAAATTGTAAAATTTCATCGACACAATTGATAAGATCAATTTGCATTAGATTTG[G/A]
TTTGTACCAGGAAATTTGGAAGCCATGTCCCTTTTCTGGCTAAGATAATCTATCTATCTATCTATCTATCTATTATATCTATCTATCTATCTATCTATCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.60%	47.30%	0.15%	0.00%	NA
All Indica	2759	83.30%	16.50%	0.14%	0.00%	NA
All Japonica	1512	0.50%	99.50%	0.00%	0.00%	NA
Aus	269	53.20%	46.10%	0.74%	0.00%	NA
Indica I	595	97.80%	2.00%	0.17%	0.00%	NA
Indica II	465	78.30%	21.70%	0.00%	0.00%	NA
Indica III	913	74.00%	25.70%	0.22%	0.00%	NA
Indica Intermediate	786	86.10%	13.70%	0.13%	0.00%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	1.00%	99.00%	0.00%	0.00%	NA
Japonica Intermediate	241	0.00%	100.00%	0.00%	0.00%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	34.40%	64.40%	1.11%	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
vg0226608386	C -> T	LOC_Os02g44080.1	3_prime_UTR_variant ; 240.0bp to feature; MODIFIER	silent_mutation	Average:43.419; most accessible tissue: Minghui63 root, score: 58.187	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0226608386	NA	4.06E-11	mr1609	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
vg0226608386	NA	1.81E-11	mr1713	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
vg0226608386	NA	2.35E-14	mr1133_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
vg0226608386	NA	1.43E-15	mr1148_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
vg0226608386	NA	1.61E-07	mr1227_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
vg0226608386	NA	1.05E-07	mr1272_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
vg0226608386	NA	6.29E-06	mr1349_2	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
vg0226608386	NA	1.43E-08	mr1479_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
vg0226608386	NA	1.58E-14	mr1726_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
vg0226608386	NA	1.18E-09	mr1835_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
vg0226608386	NA	9.10E-16	mr1836_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
vg0226608386	NA	2.93E-06	mr1871_2	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
vg0226608386	NA	1.82E-06	mr1895_2	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
vg0226608386	NA	3.64E-13	mr1904_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