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Detailed information for vg1213066313:

Variant ID: vg1213066313 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13066313
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

CGGCTAAGTGCCGTAATTCGGCCTGCAAGCTTTTGTACCTCATGTACACTTGACGGGGGCTTCATTTGCTGAATGGCGTCGATTTTCTCGGGGTTCGCTT[C/T]
GATGCCTCTTTCGGAAACCAGGAAACCCAGCAACTTGCCCGCGCGAATGCCGAAGACACACTTCTCAGGATTCAGTTTTATGCCCGCTGCGCGCAAGTTG

Reverse complement sequence

CAACTTGCGCGCAGCGGGCATAAAACTGAATCCTGAGAAGTGTGTCTTCGGCATTCGCGCGGGCAAGTTGCTGGGTTTCCTGGTTTCCGAAAGAGGCATC[G/A]
AAGCGAACCCCGAGAAAATCGACGCCATTCAGCAAATGAAGCCCCCGTCAAGTGTACATGAGGTACAAAAGCTTGCAGGCCGAATTACGGCACTTAGCCG

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	83.10%	15.50%	1.33%	0.06%	NA
All Indica	2759	95.70%	2.20%	1.96%	0.11%	NA
All Japonica	1512	60.60%	39.10%	0.33%	0.00%	NA
Aus	269	80.70%	18.60%	0.74%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	85.40%	6.20%	7.96%	0.43%	NA
Indica III	913	97.70%	1.40%	0.77%	0.11%	NA
Indica Intermediate	786	96.60%	2.20%	1.27%	0.00%	NA
Temperate Japonica	767	88.30%	11.50%	0.26%	0.00%	NA
Tropical Japonica	504	18.80%	80.80%	0.40%	0.00%	NA
Japonica Intermediate	241	59.80%	39.80%	0.41%	0.00%	NA
VI/Aromatic	96	84.40%	15.60%	0.00%	0.00%	NA
Intermediate	90	82.20%	15.60%	2.22%	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
vg1213066313	C -> DEL	LOC_Os12g23110.1	N	frameshift_variant	Average:42.737; most accessible tissue: Minghui63 flag leaf, score: 67.635	N	N	N	N
vg1213066313	C -> T	LOC_Os12g23110.1	missense_variant ; p.Glu501Lys; MODERATE	nonsynonymous_codon ; E501K	Average:42.737; most accessible tissue: Minghui63 flag leaf, score: 67.635	unknown	unknown	DELETERIOUS	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213066313	NA	6.50E-06	mr1345	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
vg1213066313	NA	4.50E-10	mr1408	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
vg1213066313	NA	2.30E-06	mr1408	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
vg1213066313	NA	2.56E-08	mr1554	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
vg1213066313	9.30E-06	9.30E-06	mr1605	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
vg1213066313	1.68E-06	2.46E-07	mr1727	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
vg1213066313	2.07E-06	NA	mr1890	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
vg1213066313	NA	4.45E-06	mr1890	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