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Detailed information for vg0406279898:

Variant ID: vg0406279898 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6279898
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

CAATGTTCCAGGAATTTGCTAACTCACAACCATCGCCGTCTGCAATCTTGAATGCACCTGGCCGCAAGACTTGCGTGATCGTGTATGGTCCTTCCCACTT[A/G]
GGTGAGAGCTCGTTACGCCCTGCTTGGCTTTGAACCCGTCGGAGGACGTAATCGCCGATCGAAAGCGTGTGTGCTCTGATGCGCTTCTCGTGGTATTGGC

Reverse complement sequence

GCCAATACCACGAGAAGCGCATCAGAGCACACACGCTTTCGATCGGCGATTACGTCCTCCGACGGGTTCAAAGCCAAGCAGGGCGTAACGAGCTCTCACC[T/C]
AAGTGGGAAGGACCATACACGATCACGCAAGTCTTGCGGCCAGGTGCATTCAAGATTGCAGACGGCGATGGTTGTGAGTTAGCAAATTCCTGGAACATTG

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	72.90%	10.40%	3.55%	13.16%	NA
All Indica	2759	82.60%	0.80%	1.12%	15.51%	NA
All Japonica	1512	59.10%	30.40%	8.47%	2.05%	NA
Aus	269	43.90%	0.00%	2.23%	53.90%	NA
Indica I	595	98.70%	0.30%	0.17%	0.84%	NA
Indica II	465	43.90%	1.70%	3.23%	51.18%	NA
Indica III	913	90.60%	0.30%	0.44%	8.65%	NA
Indica Intermediate	786	84.00%	1.10%	1.40%	13.49%	NA
Temperate Japonica	767	53.10%	35.30%	11.47%	0.13%	NA
Tropical Japonica	504	76.40%	14.30%	4.56%	4.76%	NA
Japonica Intermediate	241	41.90%	48.50%	7.05%	2.49%	NA
VI/Aromatic	96	93.80%	0.00%	1.04%	5.21%	NA
Intermediate	90	74.40%	8.90%	2.22%	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
vg0406279898	A -> DEL	LOC_Os04g11480.1	N	frameshift_variant	Average:55.344; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N
vg0406279898	A -> G	LOC_Os04g11480.1	synonymous_variant ; p.Pro540Pro; LOW	synonymous_codon	Average:55.344; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406279898	1.21E-06	6.44E-13	mr1035_2	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