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Detailed information for vg0131534483:

Variant ID: vg0131534483 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 31534483
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, C: 0.06, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

TATGAGCCGATTGATGAGTACCACAAATTCCTTCATGAACTTCGCCGGTTGCAACTTTAGCCTGATCGGCACCCAAACACTTAAGTAACACTCCATCAAT[C/T]
GTCCGGTAATAAAGCTCATCATCCAACAGAGTATACTTCAATGCCTTATATCGCAATTTCTTAGAAGCCGATTGAGACGGATTATGCAAATACTGATGCA

Reverse complement sequence

TGCATCAGTATTTGCATAATCCGTCTCAATCGGCTTCTAAGAAATTGCGATATAAGGCATTGAAGTATACTCTGTTGGATGATGAGCTTTATTACCGGAC[G/A]
ATTGATGGAGTGTTACTTAAGTGTTTGGGTGCCGATCAGGCTAAAGTTGCAACCGGCGAAGTTCATGAAGGAATTTGTGGTACTCATCAATCGGCTCATA

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	68.90%	31.10%	0.02%	0.00%	NA
All Indica	2759	97.60%	2.40%	0.04%	0.00%	NA
All Japonica	1512	17.60%	82.40%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	96.60%	3.40%	0.00%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	99.20%	0.80%	0.00%	0.00%	NA
Indica Intermediate	786	95.70%	4.20%	0.13%	0.00%	NA
Temperate Japonica	767	12.30%	87.70%	0.00%	0.00%	NA
Tropical Japonica	504	12.10%	87.90%	0.00%	0.00%	NA
Japonica Intermediate	241	46.10%	53.90%	0.00%	0.00%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	28.90%	71.10%	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
vg0131534483	C -> T	LOC_Os01g54830.1	synonymous_variant ; p.Thr1280Thr; LOW	nonsynonymous_codon ; T1280I	Average:23.438; most accessible tissue: Zhenshan97 flag leaf, score: 30.355	possibly damaging	1.632	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0131534483	NA	2.70E-07	mr1008	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
vg0131534483	NA	4.18E-07	mr1009	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
vg0131534483	NA	6.11E-11	mr1553	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
vg0131534483	NA	7.49E-11	mr1623	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
vg0131534483	NA	9.67E-08	mr1781	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
vg0131534483	7.70E-07	1.93E-10	mr1008_2	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
vg0131534483	NA	3.50E-22	mr1010_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
vg0131534483	NA	1.10E-26	mr1051_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