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Detailed information for vg0333199495:

Variant ID: vg0333199495 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 33199495
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTGCGGTCGTGAAACACCGGATTTTTGCTCAATGCAATCGCCGACTTGTTGTCAACCATCAGCTTGAAAACATCTGGTTGAGCTTGATTAATTTCTCC[C/T]
AGCAACTGTGCCATCTAGACACCCTGACATGCTACCGTCGTCGCCGCAATATACTCTGCCTCGCAAGACGAAAGAGCGACAACCTTTTGCTTCTGGGATT

Reverse complement sequence

AATCCCAGAAGCAAAAGGTTGTCGCTCTTTCGTCTTGCGAGGCAGAGTATATTGCGGCGACGACGGTAGCATGTCAGGGTGTCTAGATGGCACAGTTGCT[G/A]
GGAGAAATTAATCAAGCTCAACCAGATGTTTTCAAGCTGATGGTTGACAACAAGTCGGCGATTGCATTGAGCAAAAATCCGGTGTTTCACGACCGCAGAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.40%	49.00%	0.15%	0.47%	NA
All Indica	2759	25.60%	73.50%	0.14%	0.69%	NA
All Japonica	1512	99.50%	0.30%	0.07%	0.13%	NA
Aus	269	5.60%	94.40%	0.00%	0.00%	NA
Indica I	595	13.40%	85.50%	0.17%	0.84%	NA
Indica II	465	56.10%	42.20%	0.65%	1.08%	NA
Indica III	913	13.30%	86.50%	0.00%	0.22%	NA
Indica Intermediate	786	31.20%	67.90%	0.00%	0.89%	NA
Temperate Japonica	767	99.60%	0.10%	0.13%	0.13%	NA
Tropical Japonica	504	99.40%	0.40%	0.00%	0.20%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	67.80%	28.90%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0333199495	C -> T	LOC_Os03g58270.1	synonymous_variant ; p.Leu1096Leu; LOW	synonymous_codon	Average:52.095; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N
vg0333199495	C -> DEL	LOC_Os03g58270.1	N	frameshift_variant	Average:52.095; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0333199495	NA	1.51E-12	mr1069	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
vg0333199495	NA	3.87E-15	mr1441	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
vg0333199495	5.40E-09	1.62E-37	mr1723	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
vg0333199495	5.92E-08	7.61E-10	mr1723	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
vg0333199495	NA	3.57E-07	mr1062_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
vg0333199495	NA	1.00E-26	mr1441_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
vg0333199495	5.30E-12	4.87E-43	mr1723_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
vg0333199495	4.93E-10	7.52E-13	mr1723_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