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Detailed information for vg0228204274:

Variant ID: vg0228204274 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 28204274
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCGCCCTAGGGCCAAGCCTGTGCTCTGATACCATCTCTTGTCACGCCCCGAACTAGTACCGACCGGAACTAGCCCGCGACGCTCCAAATTAACCTGTTA[G/A]
TTGATACCAGTCCCAAGAAACAGTGCTGGTATCACAGGAAGACAGATTATCACAGCAACAGAGGTCTCTTTATTATAGAGTAGAGGTACAGTCATGTTGG

Reverse complement sequence

CCAACATGACTGTACCTCTACTCTATAATAAAGAGACCTCTGTTGCTGTGATAATCTGTCTTCCTGTGATACCAGCACTGTTTCTTGGGACTGGTATCAA[C/T]
TAACAGGTTAATTTGGAGCGTCGCGGGCTAGTTCCGGTCGGTACTAGTTCGGGGCGTGACAAGAGATGGTATCAGAGCACAGGCTTGGCCCTAGGGCGAA

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	38.00%	2.30%	18.03%	41.66%	NA
All Indica	2759	4.20%	0.70%	26.64%	68.39%	NA
All Japonica	1512	93.90%	5.40%	0.20%	0.46%	NA
Aus	269	41.30%	0.40%	39.41%	18.96%	NA
Indica I	595	3.70%	0.20%	3.87%	92.27%	NA
Indica II	465	4.50%	1.90%	44.73%	48.82%	NA
Indica III	913	2.50%	0.70%	36.04%	60.79%	NA
Indica Intermediate	786	6.50%	0.50%	22.26%	70.74%	NA
Temperate Japonica	767	97.80%	1.80%	0.00%	0.39%	NA
Tropical Japonica	504	85.70%	13.10%	0.40%	0.79%	NA
Japonica Intermediate	241	98.80%	0.80%	0.41%	0.00%	NA
VI/Aromatic	96	92.70%	6.20%	1.04%	0.00%	NA
Intermediate	90	63.30%	2.20%	7.78%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0228204274	G -> A	LOC_Os02g46240.1	upstream_gene_variant ; 1872.0bp to feature; MODIFIER	silent_mutation	Average:10.156; most accessible tissue: Minghui63 root, score: 15.664	N	N	N	N
vg0228204274	G -> A	LOC_Os02g46250.1	upstream_gene_variant ; 238.0bp to feature; MODIFIER	silent_mutation	Average:10.156; most accessible tissue: Minghui63 root, score: 15.664	N	N	N	N
vg0228204274	G -> A	LOC_Os02g46250-LOC_Os02g46260	intergenic_region ; MODIFIER	silent_mutation	Average:10.156; most accessible tissue: Minghui63 root, score: 15.664	N	N	N	N
vg0228204274	G -> DEL	N	N	silent_mutation	Average:10.156; most accessible tissue: Minghui63 root, score: 15.664	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0228204274	NA	4.82E-77	mr1629	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
vg0228204274	NA	1.07E-10	mr1751	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
vg0228204274	NA	2.02E-25	mr1051_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
vg0228204274	NA	2.40E-06	mr1329_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
vg0228204274	1.44E-07	3.82E-21	mr1342_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
vg0228204274	1.83E-12	7.91E-105	mr1629_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
vg0228204274	7.89E-07	NA	mr1789_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
vg0228204274	3.26E-07	1.72E-09	mr1905_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