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Detailed information for vg0139966045:

Variant ID: vg0139966045 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 39966045
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

TAAGATTTTCATGCAGCTTCTTTATTTCTGCATCATAACGATCTTTGGGGAAATGAAGATCATATAGTGTTAACCCCCAGAAAGTAGCATATAAATCAGG[T/C]
GATAAACCATTCCAGGTTTTTGCTGGGAAAGTGTTCCGGACTGTGCTAAGAAGATCAGACCACCTGCACCAAAACAGAATACATTGAGTATGTAAAATAC

Reverse complement sequence

GTATTTTACATACTCAATGTATTCTGTTTTGGTGCAGGTGGTCTGATCTTCTTAGCACAGTCCGGAACACTTTCCCAGCAAAAACCTGGAATGGTTTATC[A/G]
CCTGATTTATATGCTACTTTCTGGGGGTTAACACTATATGATCTTCATTTCCCCAAAGATCGTTATGATGCAGAAATAAAGAAGCTGCATGAAAATCTTA

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	93.10%	6.90%	0.00%	0.00%	NA
All Indica	2759	99.70%	0.30%	0.00%	0.00%	NA
All Japonica	1512	79.60%	20.40%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.40%	0.00%	0.00%	NA
Temperate Japonica	767	77.20%	22.80%	0.00%	0.00%	NA
Tropical Japonica	504	85.10%	14.90%	0.00%	0.00%	NA
Japonica Intermediate	241	75.50%	24.50%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	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
vg0139966045	T -> C	LOC_Os01g68810.1	synonymous_variant ; p.Ser951Ser; LOW	synonymous_codon	Average:49.047; most accessible tissue: Callus, score: 81.39	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0139966045	5.80E-06	NA	mr1154	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
vg0139966045	9.22E-07	1.03E-07	mr1154	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
vg0139966045	3.65E-06	8.21E-07	mr1092_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