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Detailed information for vg0228568193:

Variant ID: vg0228568193 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 28568193
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCACGGTTTTTATATCGGAAAACTCAAATCATCCCTTTTATATCGCTCTCTGTCCTTTGGATGATTAAAAGTAAGCTACTCCCTCCGTTTCGAAATGTTT[G/A]
ACACCGTTGATTTTTTAGCATATGTTTGACCGTTCGTCTTATTCAAAAACTTTTGTGAAATATGTAAAATTATATGCCTACATAAAAATATATTTAACAA

Reverse complement sequence

TTGTTAAATATATTTTTATGTAGGCATATAATTTTACATATTTCACAAAAGTTTTTGAATAAGACGAACGGTCAAACATATGCTAAAAAATCAACGGTGT[C/T]
AAACATTTCGAAACGGAGGGAGTAGCTTACTTTTAATCATCCAAAGGACAGAGAGCGATATAAAAGGGATGATTTGAGTTTTCCGATATAAAAACCGTGC

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	40.10%	6.80%	0.15%	53.00%	NA
All Indica	2759	10.40%	0.50%	0.11%	88.98%	NA
All Japonica	1512	79.90%	19.60%	0.26%	0.20%	NA
Aus	269	92.90%	0.00%	0.00%	7.06%	NA
Indica I	595	1.70%	0.00%	0.17%	98.15%	NA
Indica II	465	6.70%	0.40%	0.22%	92.69%	NA
Indica III	913	13.80%	0.50%	0.00%	85.65%	NA
Indica Intermediate	786	15.30%	0.90%	0.13%	83.72%	NA
Temperate Japonica	767	87.70%	12.10%	0.00%	0.13%	NA
Tropical Japonica	504	62.90%	35.90%	0.79%	0.40%	NA
Japonica Intermediate	241	90.50%	9.50%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	60.00%	10.00%	0.00%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0228568193	G -> A	LOC_Os02g46790.1	downstream_gene_variant ; 813.0bp to feature; MODIFIER	silent_mutation	Average:43.498; most accessible tissue: Callus, score: 75.035	N	N	N	N
vg0228568193	G -> A	LOC_Os02g46800.1	downstream_gene_variant ; 4714.0bp to feature; MODIFIER	silent_mutation	Average:43.498; most accessible tissue: Callus, score: 75.035	N	N	N	N
vg0228568193	G -> A	LOC_Os02g46790-LOC_Os02g46800	intergenic_region ; MODIFIER	silent_mutation	Average:43.498; most accessible tissue: Callus, score: 75.035	N	N	N	N
vg0228568193	G -> DEL	N	N	silent_mutation	Average:43.498; most accessible tissue: Callus, score: 75.035	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0228568193	NA	3.92E-10	mr1379_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
vg0228568193	NA	4.13E-10	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
vg0228568193	3.65E-06	NA	mr1923_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