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Detailed information for vg0401502812:

Variant ID: vg0401502812 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1502812
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTGTTGTGTCTACTGAGCCGGAAGTTCTGGGTCCTATTGACCGAAACCTCCAGACATCTCCAGGCCCGGAAGTTCCGGGTTCTACAGTCCGGAACCTCT[G/A]
GACCAGTGGCAGTGAAGATGTGCCAACGGCACAAGTGGATGGGATCGATGCTGCGGGCACTTTAGAGCATACTGATCAGGCTCAGGTCCCTCCAGTGCAC

Reverse complement sequence

GTGCACTGGAGGGACCTGAGCCTGATCAGTATGCTCTAAAGTGCCCGCAGCATCGATCCCATCCACTTGTGCCGTTGGCACATCTTCACTGCCACTGGTC[C/T]
AGAGGTTCCGGACTGTAGAACCCGGAACTTCCGGGCCTGGAGATGTCTGGAGGTTTCGGTCAATAGGACCCAGAACTTCCGGCTCAGTAGACACAACACT

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	95.80%	0.50%	0.42%	3.28%	NA
All Indica	2759	98.90%	0.80%	0.29%	0.07%	NA
All Japonica	1512	89.30%	0.00%	0.73%	9.99%	NA
Aus	269	98.50%	0.70%	0.37%	0.37%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.60%	0.20%	0.22%	0.00%	NA
Indica III	913	98.60%	1.30%	0.11%	0.00%	NA
Indica Intermediate	786	98.10%	1.00%	0.64%	0.25%	NA
Temperate Japonica	767	89.20%	0.00%	0.39%	10.43%	NA
Tropical Japonica	504	89.70%	0.00%	1.59%	8.73%	NA
Japonica Intermediate	241	88.80%	0.00%	0.00%	11.20%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	98.90%	1.10%	0.00%	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
vg0401502812	G -> DEL	LOC_Os04g03470.1	N	frameshift_variant	Average:16.109; most accessible tissue: Callus, score: 33.69	N	N	N	N
vg0401502812	G -> A	LOC_Os04g03470.1	stop_gained ; p.Trp1091*; HIGH	stop_gained	Average:16.109; most accessible tissue: Callus, score: 33.69	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401502812	NA	3.14E-06	mr1254	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
vg0401502812	2.89E-06	2.89E-06	mr1275	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
vg0401502812	NA	8.75E-06	mr1986	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
vg0401502812	NA	7.47E-06	mr1860_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