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Detailed information for vg0609018547:

Variant ID: vg0609018547 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 9018547
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, A: 0.03, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

CAACCCTCTAACATACTAGATGGATGAACACAAAGCTCAAATGAGTGTGAGAGAGGTGCAAGGGGTGTATGCAATTGAATTGGGTGCCAAGAGAGCCCCC[T/A]
TGCAGCTGGTGGGGGAGTATTTATACTCCCACCCACCAAAACTAGCCGTTAGGGGCGAAATCCCCAAACTTTGTGCTCTGCCGGTCTGACCGAAGGTATG

Reverse complement sequence

CATACCTTCGGTCAGACCGGCAGAGCACAAAGTTTGGGGATTTCGCCCCTAACGGCTAGTTTTGGTGGGTGGGAGTATAAATACTCCCCCACCAGCTGCA[A/T]
GGGGGCTCTCTTGGCACCCAATTCAATTGCATACACCCCTTGCACCTCTCTCACACTCATTTGAGCTTTGTGTTCATCCATCTAGTATGTTAGAGGGTTG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.20%	17.50%	1.63%	3.68%	NA
All Indica	2759	69.40%	29.70%	0.51%	0.36%	NA
All Japonica	1512	99.80%	0.10%	0.07%	0.07%	NA
Aus	269	19.30%	0.40%	22.30%	57.99%	NA
Indica I	595	60.80%	38.80%	0.34%	0.00%	NA
Indica II	465	94.80%	4.90%	0.22%	0.00%	NA
Indica III	913	56.30%	43.40%	0.22%	0.11%	NA
Indica Intermediate	786	76.20%	21.50%	1.15%	1.15%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	94.80%	0.00%	2.08%	3.12%	NA
Intermediate	90	87.80%	7.80%	0.00%	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
vg0609018547	T -> A	LOC_Os06g15880.1	missense_variant ; p.Leu80Met; MODERATE	nonsynonymous_codon ; L80M	Average:37.717; most accessible tissue: Zhenshan97 flag leaf, score: 83.84	unknown	unknown	TOLERATED	0.25
vg0609018547	T -> DEL	LOC_Os06g15880.1	N	frameshift_variant	Average:37.717; most accessible tissue: Zhenshan97 flag leaf, score: 83.84	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0609018547	6.72E-06	1.63E-08	mr1570	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
vg0609018547	3.76E-06	5.19E-09	mr1570	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
vg0609018547	NA	4.27E-07	mr1570_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
vg0609018547	NA	4.00E-07	mr1668_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
vg0609018547	NA	2.24E-06	mr1668_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