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Detailed information for vg1220128766:

Variant ID: vg1220128766 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 20128766
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:

CCATGGCGACAATCCAGAAGCAGAATACCGCCATCCAAGCTTCGATGGGATCCTTGGAGGAAATCAAGCCTATGGTGGTGGAACTCGCGAGCTGGAAGCC[A/G]
GCGGTGGACAAGGCCATGACGGAGATGCGGGACGACCTCGGCGACCTGCGTCAGCAAGTGGAGCGGATATCCCGCAATCCGATTCTCGCCGTCAAGCCAG

Reverse complement sequence

CTGGCTTGACGGCGAGAATCGGATTGCGGGATATCCGCTCCACTTGCTGACGCAGGTCGCCGAGGTCGTCCCGCATCTCCGTCATGGCCTTGTCCACCGC[T/C]
GGCTTCCAGCTCGCGAGTTCCACCACCATAGGCTTGATTTCCTCCAAGGATCCCATCGAAGCTTGGATGGCGGTATTCTGCTTCTGGATTGTCGCCATGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	39.40%	13.20%	38.62%	8.74%	NA
All Indica	2759	27.90%	19.80%	46.32%	5.94%	NA
All Japonica	1512	65.50%	1.70%	19.05%	13.76%	NA
Aus	269	19.70%	10.40%	69.52%	0.37%	NA
Indica I	595	9.60%	31.30%	51.93%	7.23%	NA
Indica II	465	38.30%	10.50%	42.15%	9.03%	NA
Indica III	913	38.60%	20.00%	38.23%	3.18%	NA
Indica Intermediate	786	23.30%	16.40%	53.94%	6.36%	NA
Temperate Japonica	767	93.60%	0.10%	2.74%	3.52%	NA
Tropical Japonica	504	24.80%	4.60%	47.42%	23.21%	NA
Japonica Intermediate	241	61.00%	0.80%	11.62%	26.56%	NA
VI/Aromatic	96	8.30%	14.60%	39.58%	37.50%	NA
Intermediate	90	46.70%	11.10%	37.78%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1220128766	A -> DEL	LOC_Os12g33280.1	N	frameshift_variant	Average:27.198; most accessible tissue: Callus, score: 47.912	N	N	N	N
vg1220128766	A -> G	LOC_Os12g33280.1	synonymous_variant ; p.Pro44Pro; LOW	synonymous_codon	Average:27.198; most accessible tissue: Callus, score: 47.912	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1220128766	NA	6.73E-10	mr1093	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
vg1220128766	NA	4.58E-06	mr1179	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
vg1220128766	1.55E-21	NA	mr1334	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
vg1220128766	1.80E-09	1.08E-08	mr1334	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
vg1220128766	5.12E-11	8.80E-26	mr1334	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
vg1220128766	NA	3.43E-09	mr1403	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
vg1220128766	NA	1.75E-07	mr1599	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
vg1220128766	NA	9.56E-08	mr1733	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
vg1220128766	7.68E-06	7.68E-06	mr1987	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
vg1220128766	1.71E-13	NA	mr1334_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
vg1220128766	4.56E-11	4.73E-32	mr1334_2	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
vg1220128766	3.90E-06	NA	mr1991_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
vg1220128766	5.71E-09	3.26E-15	mr1991_2	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