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Detailed information for vg1204319901:

Variant ID: vg1204319901 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4319901
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 39. )

Flanking Sequence (100 bp) in Reference Genome:

TCTCAACGAAGTCTGGTGGATCGGCTGCTGAAGCTGCTGCCTTGGTGGTGTCTGCTGAATCGGTTGCAGAGGCTGCTGCCTTGTTGGTATTTGCTGAGCA[G/A]
GTTGTACGACCTGTTGTTGGATTGGTTGTACAACCGGCTGGATTGGCGGCGTCTGCTGAACCGGCTGCTGCTGCACTGGATCAACAATAGGTGGAGGTGG

Reverse complement sequence

CCACCTCCACCTATTGTTGATCCAGTGCAGCAGCAGCCGGTTCAGCAGACGCCGCCAATCCAGCCGGTTGTACAACCAATCCAACAACAGGTCGTACAAC[C/T]
TGCTCAGCAAATACCAACAAGGCAGCAGCCTCTGCAACCGATTCAGCAGACACCACCAAGGCAGCAGCTTCAGCAGCCGATCCACCAGACTTCGTTGAGA

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	38.10%	27.10%	13.77%	21.01%	NA
All Indica	2759	39.70%	8.10%	19.14%	33.09%	NA
All Japonica	1512	31.50%	57.60%	6.48%	4.43%	NA
Aus	269	45.00%	50.90%	4.09%	0.00%	NA
Indica I	595	18.30%	9.70%	12.94%	58.99%	NA
Indica II	465	29.20%	9.70%	19.35%	41.72%	NA
Indica III	913	60.90%	2.40%	22.89%	13.80%	NA
Indica Intermediate	786	37.40%	12.50%	19.34%	30.79%	NA
Temperate Japonica	767	9.30%	83.70%	2.61%	4.43%	NA
Tropical Japonica	504	55.20%	27.60%	12.70%	4.56%	NA
Japonica Intermediate	241	52.70%	37.30%	5.81%	4.15%	NA
VI/Aromatic	96	80.20%	17.70%	2.08%	0.00%	NA
Intermediate	90	36.70%	35.60%	13.33%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1204319901	G -> DEL	LOC_Os12g08510.1	N	frameshift_variant	Average:10.045; most accessible tissue: Zhenshan97 young leaf, score: 24.604	N	N	N	N
vg1204319901	G -> A	LOC_Os12g08510.1	missense_variant ; p.Pro283Leu; MODERATE	nonsynonymous_codon ; P283L	Average:10.045; most accessible tissue: Zhenshan97 young leaf, score: 24.604	unknown	unknown	DELETERIOUS	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204319901	4.00E-06	4.00E-06	mr1688	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