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Detailed information for vg1214642471:

Variant ID: vg1214642471 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14642471
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

AGTACTGGTCGAAGTAGTAATTTCTGGAGGACCATTTCGATCAGCATCAACAGTACCCGAACCCGACGACCCTGGCTGGTCTGACCGCTCCTCATGGGCC[G/A]
GTCTGACCGGAGGTGTGCCGGCGGTCTGACCGGCCTGGCGCCCGGTCTGACCGGCCGAGCTGACCTCGTCGTCGTCGTTGTCTCCGCTCTCGTCTTCAAA

Reverse complement sequence

TTTGAAGACGAGAGCGGAGACAACGACGACGACGAGGTCAGCTCGGCCGGTCAGACCGGGCGCCAGGCCGGTCAGACCGCCGGCACACCTCCGGTCAGAC[C/T]
GGCCCATGAGGAGCGGTCAGACCAGCCAGGGTCGTCGGGTTCGGGTACTGTTGATGCTGATCGAAATGGTCCTCCAGAAATTACTACTTCGACCAGTACT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.00%	1.60%	7.02%	13.42%	NA
All Indica	2759	65.10%	1.60%	10.80%	22.47%	NA
All Japonica	1512	96.60%	1.50%	1.59%	0.26%	NA
Aus	269	97.40%	1.50%	1.12%	0.00%	NA
Indica I	595	52.30%	2.50%	30.92%	14.29%	NA
Indica II	465	63.90%	3.70%	5.59%	26.88%	NA
Indica III	913	69.00%	0.50%	1.97%	28.48%	NA
Indica Intermediate	786	71.00%	1.00%	8.91%	19.08%	NA
Temperate Japonica	767	99.00%	0.10%	0.52%	0.39%	NA
Tropical Japonica	504	94.40%	3.40%	2.18%	0.00%	NA
Japonica Intermediate	241	93.80%	2.10%	3.73%	0.41%	NA
VI/Aromatic	96	85.40%	2.10%	4.17%	8.33%	NA
Intermediate	90	94.40%	0.00%	3.33%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1214642471	G -> DEL	LOC_Os12g25380.1	N	frameshift_variant	Average:20.933; most accessible tissue: Callus, score: 36.725	N	N	N	N
vg1214642471	G -> A	LOC_Os12g25380.1	missense_variant ; p.Pro567Leu; MODERATE	nonsynonymous_codon ; P567L	Average:20.933; most accessible tissue: Callus, score: 36.725	unknown	unknown	DELETERIOUS	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214642471	NA	3.00E-07	mr1186	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
vg1214642471	1.89E-07	1.89E-07	mr1499	Jap_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
vg1214642471	NA	4.60E-06	mr1616	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
vg1214642471	3.57E-06	3.57E-06	mr1943	Jap_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
vg1214642471	NA	3.67E-06	mr1308_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
vg1214642471	NA	1.46E-06	mr1361_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