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Detailed information for vg0209228990:

Variant ID: vg0209228990 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 9228990
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACCTTTGGTAGCATGGTTAATACCTACAGGTTTTAGACTTGGTATAGGTACCAACCAATATCACATAGGTACCAAGTACAAGGTATAACGTGCGTCACT[G/A]
CCGCTTGGGCAGGTGGTGAGCTGTCGACCACCAGCGTTTTGTCTCGTCTTCTCCCTTCTATTCCTTTCCAAATCTCCATGCCTTTTCTTCTCAATCTGGT

Reverse complement sequence

ACCAGATTGAGAAGAAAAGGCATGGAGATTTGGAAAGGAATAGAAGGGAGAAGACGAGACAAAACGCTGGTGGTCGACAGCTCACCACCTGCCCAAGCGG[C/T]
AGTGACGCACGTTATACCTTGTACTTGGTACCTATGTGATATTGGTTGGTACCTATACCAAGTCTAAAACCTGTAGGTATTAACCATGCTACCAAAGGTA

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	42.30%	1.20%	1.10%	55.40%	NA
All Indica	2759	14.70%	0.00%	1.63%	83.65%	NA
All Japonica	1512	93.40%	3.70%	0.20%	2.71%	NA
Aus	269	15.60%	0.00%	0.37%	84.01%	NA
Indica I	595	27.70%	0.00%	3.70%	68.57%	NA
Indica II	465	20.00%	0.00%	0.65%	79.35%	NA
Indica III	913	3.60%	0.00%	0.77%	95.62%	NA
Indica Intermediate	786	14.60%	0.00%	1.65%	83.72%	NA
Temperate Japonica	767	91.80%	6.00%	0.39%	1.83%	NA
Tropical Japonica	504	96.00%	0.00%	0.00%	3.97%	NA
Japonica Intermediate	241	92.90%	4.10%	0.00%	2.90%	NA
VI/Aromatic	96	88.50%	0.00%	1.04%	10.42%	NA
Intermediate	90	61.10%	0.00%	2.22%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0209228990	G -> A	LOC_Os02g16240.1	downstream_gene_variant ; 4944.0bp to feature; MODIFIER	silent_mutation	Average:10.643; most accessible tissue: Callus, score: 53.164	N	N	N	N
vg0209228990	G -> A	LOC_Os02g16230-LOC_Os02g16240	intergenic_region ; MODIFIER	silent_mutation	Average:10.643; most accessible tissue: Callus, score: 53.164	N	N	N	N
vg0209228990	G -> DEL	N	N	silent_mutation	Average:10.643; most accessible tissue: Callus, score: 53.164	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0209228990	NA	3.19E-06	mr1057	Jap_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
vg0209228990	NA	1.47E-06	mr1210	Jap_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
vg0209228990	NA	8.36E-06	mr1305	Jap_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
vg0209228990	NA	7.08E-06	mr1586	Jap_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
vg0209228990	2.70E-06	2.70E-06	mr1166_2	Jap_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
vg0209228990	8.61E-09	8.51E-10	mr1305_2	Jap_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
vg0209228990	7.07E-07	6.67E-09	mr1585_2	Jap_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