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Detailed information for vg1206760481:

Variant ID: vg1206760481 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 6760481
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.69, G: 0.33, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

GAGCCTGGATATGGAAGTGGGAACAAGGCCTTCGGCGCAAACGAATTGAAACCATTGGAAAGATCCTGGTCAGTTTGATCAGTTTCAGCTGCCGGCTGTG[G/C]
AGGCGGCTGGGATGGTTCGGAGGAATGATCAGGCGACATGTCTTCTTCAGGTATATCTAGTACTGCGGGTGCGTCTTCTTGCCCTTTGGGCTTCGAAGGA

Reverse complement sequence

TCCTTCGAAGCCCAAAGGGCAAGAAGACGCACCCGCAGTACTAGATATACCTGAAGAAGACATGTCGCCTGATCATTCCTCCGAACCATCCCAGCCGCCT[C/G]
CACAGCCGGCAGCTGAAACTGATCAAACTGACCAGGATCTTTCCAATGGTTTCAATTCGTTTGCGCCGAAGGCCTTGTTCCCACTTCCATATCCAGGCTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.80%	33.80%	0.11%	0.32%	NA
All Indica	2759	46.50%	52.90%	0.14%	0.51%	NA
All Japonica	1512	96.60%	3.40%	0.00%	0.00%	NA
Aus	269	81.40%	18.60%	0.00%	0.00%	NA
Indica I	595	97.10%	2.70%	0.00%	0.17%	NA
Indica II	465	23.70%	75.10%	0.43%	0.86%	NA
Indica III	913	19.20%	80.60%	0.00%	0.22%	NA
Indica Intermediate	786	53.30%	45.50%	0.25%	0.89%	NA
Temperate Japonica	767	95.30%	4.70%	0.00%	0.00%	NA
Tropical Japonica	504	97.60%	2.40%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	74.00%	25.00%	0.00%	1.04%	NA
Intermediate	90	83.30%	15.60%	1.11%	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
vg1206760481	G -> C	LOC_Os12g12300.1	missense_variant ; p.Pro306Ala; MODERATE	nonsynonymous_codon ; P306A	Average:76.501; most accessible tissue: Callus, score: 86.695	unknown	unknown	DELETERIOUS	0.03
vg1206760481	G -> DEL	LOC_Os12g12300.1	N	frameshift_variant	Average:76.501; most accessible tissue: Callus, score: 86.695	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1206760481	NA	1.93E-10	Grain_width	Ind_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1206760481	3.37E-06	NA	mr1024	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
vg1206760481	NA	3.58E-09	mr1336	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
vg1206760481	NA	8.46E-14	mr1565	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
vg1206760481	4.97E-06	4.26E-06	mr1940	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
vg1206760481	NA	1.74E-06	mr1024_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
vg1206760481	NA	3.59E-17	mr1565_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
vg1206760481	NA	3.96E-11	mr1565_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
vg1206760481	NA	4.39E-08	mr1861_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