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Detailed information for vg1207352636:

Variant ID: vg1207352636 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 7352636
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

AATGGTTCACATTTCCGGCTAAAGCAAATGATAGGCTTAAGCGGAAGGCATTCCAGAGGATGGGCAAAGCTTGGAAGAATTGGAAGTCGAAGCTCTTCAC[T/C]
GAGTTTGTCAACCCGCCCGGCAATCATACGCCGTTCGATGAATACCCTCAAATAACCGAAGCGGTGTGGGAGGAATTCTGCTCTCTCAAGAACACCCAAG

Reverse complement sequence

CTTGGGTGTTCTTGAGAGAGCAGAATTCCTCCCACACCGCTTCGGTTATTTGAGGGTATTCATCGAACGGCGTATGATTGCCGGGCGGGTTGACAAACTC[A/G]
GTGAAGAGCTTCGACTTCCAATTCTTCCAAGCTTTGCCCATCCTCTGGAATGCCTTCCGCTTAAGCCTATCATTTGCTTTAGCCGGAAATGTGAACCATT

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	63.20%	36.60%	0.19%	0.00%	NA
All Indica	2759	95.30%	4.50%	0.22%	0.00%	NA
All Japonica	1512	5.00%	95.00%	0.07%	0.00%	NA
Aus	269	75.80%	24.20%	0.00%	0.00%	NA
Indica I	595	95.30%	4.40%	0.34%	0.00%	NA
Indica II	465	95.50%	4.30%	0.22%	0.00%	NA
Indica III	913	97.50%	2.30%	0.22%	0.00%	NA
Indica Intermediate	786	92.70%	7.10%	0.13%	0.00%	NA
Temperate Japonica	767	5.10%	94.80%	0.13%	0.00%	NA
Tropical Japonica	504	5.80%	94.20%	0.00%	0.00%	NA
Japonica Intermediate	241	2.90%	97.10%	0.00%	0.00%	NA
VI/Aromatic	96	53.10%	44.80%	2.08%	0.00%	NA
Intermediate	90	32.20%	67.80%	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
vg1207352636	T -> C	LOC_Os12g13200.1	synonymous_variant ; p.Thr101Thr; LOW	synonymous_codon	Average:43.172; most accessible tissue: Zhenshan97 flag leaf, score: 60.074	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1207352636	2.01E-06	6.71E-06	mr1609	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
vg1207352636	NA	1.25E-25	mr1024_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
vg1207352636	NA	9.09E-21	mr1298_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
vg1207352636	NA	2.30E-14	mr1529_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
vg1207352636	NA	1.09E-13	mr1575_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
vg1207352636	NA	4.87E-07	mr1604_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
vg1207352636	NA	1.72E-19	mr1731_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
vg1207352636	NA	4.95E-20	mr1922_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
vg1207352636	NA	3.14E-08	mr1940_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