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Detailed information for vg0334753499:

Variant ID: vg0334753499 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 34753499
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

TTAAAACATAATCCTTGTGCTCTCCGGTACTCTTTCAACTGCTGAGCCTTCCACAATTCACCAGGAGCCAACTTCTGTTTCTCTCCACCTCGTCCCACCT[G/A]
AAAGTTCTTCTTAGAAACAGATTTCTTACTCCCAGAACTAGGCAAAGCACTCTCATAAGCTAGAGCCACTAAGAAAGCTTGTGTGACTGAAGTGGGTTGT

Reverse complement sequence

ACAACCCACTTCAGTCACACAAGCTTTCTTAGTGGCTCTAGCTTATGAGAGTGCTTTGCCTAGTTCTGGGAGTAAGAAATCTGTTTCTAAGAAGAACTTT[C/T]
AGGTGGGACGAGGTGGAGAGAAACAGAAGTTGGCTCCTGGTGAATTGTGGAAGGCTCAGCAGTTGAAAGAGTACCGGAGAGCACAAGGATTATGTTTTAA

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	93.80%	3.50%	2.22%	0.44%	NA
All Indica	2759	91.70%	4.00%	3.59%	0.76%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.00%	NA
Aus	269	79.20%	19.70%	1.12%	0.00%	NA
Indica I	595	69.60%	14.60%	13.11%	2.69%	NA
Indica II	465	98.50%	0.00%	1.51%	0.00%	NA
Indica III	913	99.10%	0.70%	0.11%	0.11%	NA
Indica Intermediate	786	95.80%	2.00%	1.65%	0.51%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	95.60%	3.30%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0334753499	G -> A	LOC_Os03g61190.1	stop_gained ; p.Gln315*; HIGH	stop_gained	Average:64.737; most accessible tissue: Zhenshan97 young leaf, score: 82.539	N	N	N	N
vg0334753499	G -> DEL	LOC_Os03g61190.1	N	frameshift_variant	Average:64.737; most accessible tissue: Zhenshan97 young leaf, score: 82.539	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0334753499	3.44E-06	NA	mr1151	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
vg0334753499	NA	7.00E-06	mr1585	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