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Detailed information for vg1214075681:

Variant ID: vg1214075681 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14075681
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.08, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

GCCAGGCCGGTCAGACCGCCGGCACACCTCCGGTCAGACCGCCTCAGGAGGAGCAGTCAGACCGGCCAGGAATGTCGGGTTCGGGTCTGTTGATGCTGAT[C/T]
GAGATGGTCCTCCGGAGATTACTACTTCGACCAGTACTGATACAGAACGTGGATCAACTTCAGAAGTCGCTGCTCCTTTGCACATTCAACGTCGACATTC

Reverse complement sequence

GAATGTCGACGTTGAATGTGCAAAGGAGCAGCGACTTCTGAAGTTGATCCACGTTCTGTATCAGTACTGGTCGAAGTAGTAATCTCCGGAGGACCATCTC[G/A]
ATCAGCATCAACAGACCCGAACCCGACATTCCTGGCCGGTCTGACTGCTCCTCCTGAGGCGGTCTGACCGGAGGTGTGCCGGCGGTCTGACCGGCCTGGC

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	74.90%	25.00%	0.08%	0.00%	NA
All Indica	2759	78.80%	21.10%	0.11%	0.00%	NA
All Japonica	1512	67.50%	32.50%	0.07%	0.00%	NA
Aus	269	81.80%	18.20%	0.00%	0.00%	NA
Indica I	595	66.60%	33.10%	0.34%	0.00%	NA
Indica II	465	84.10%	15.90%	0.00%	0.00%	NA
Indica III	913	84.90%	15.10%	0.00%	0.00%	NA
Indica Intermediate	786	77.70%	22.10%	0.13%	0.00%	NA
Temperate Japonica	767	88.30%	11.70%	0.00%	0.00%	NA
Tropical Japonica	504	36.90%	63.10%	0.00%	0.00%	NA
Japonica Intermediate	241	65.10%	34.40%	0.41%	0.00%	NA
VI/Aromatic	96	75.00%	25.00%	0.00%	0.00%	NA
Intermediate	90	63.30%	36.70%	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
vg1214075681	C -> T	LOC_Os12g24600.1	synonymous_variant ; p.Ile995Ile; LOW	synonymous_codon	Average:47.798; most accessible tissue: Minghui63 young leaf, score: 73.49	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214075681	NA	6.79E-10	mr1224	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
vg1214075681	NA	4.55E-08	mr1225	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
vg1214075681	7.44E-06	NA	mr1284	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