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Detailed information for vg0111348696:

Variant ID: vg0111348696 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 11348696
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTTGGTGCGGGGTCTTATGCACGAGACAAGGATACGTCAAAAAGCTGGATTTTTCACATTTTGGTCCTTTTAAAAAACTTATTTCGTAAATAGACCCCT[G/A]
AAAAAACTTATCCCAAAAATAGTCCTTTTTGGGGCGCCAGAGTGGCTGGCGCCGTCGTTCAACAGGACGGCGCCAGCCTCTTTGGCGCCGTCCCCCTGCC

Reverse complement sequence

GGCAGGGGGACGGCGCCAAAGAGGCTGGCGCCGTCCTGTTGAACGACGGCGCCAGCCACTCTGGCGCCCCAAAAAGGACTATTTTTGGGATAAGTTTTTT[C/T]
AGGGGTCTATTTACGAAATAAGTTTTTTAAAAGGACCAAAATGTGAAAAATCCAGCTTTTTGACGTATCCTTGTCTCGTGCATAAGACCCCGCACCAAAA

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	39.70%	0.10%	16.12%	44.01%	NA
All Indica	2759	11.60%	0.10%	21.96%	66.29%	NA
All Japonica	1512	97.00%	0.10%	0.13%	2.78%	NA
Aus	269	4.50%	1.10%	52.42%	42.01%	NA
Indica I	595	23.50%	0.00%	3.87%	72.61%	NA
Indica II	465	17.00%	0.00%	17.20%	65.81%	NA
Indica III	913	1.90%	0.30%	38.88%	58.93%	NA
Indica Intermediate	786	10.80%	0.00%	18.83%	70.36%	NA
Temperate Japonica	767	98.80%	0.00%	0.13%	1.04%	NA
Tropical Japonica	504	93.80%	0.20%	0.20%	5.75%	NA
Japonica Intermediate	241	97.90%	0.00%	0.00%	2.07%	NA
VI/Aromatic	96	34.40%	0.00%	2.08%	63.54%	NA
Intermediate	90	48.90%	0.00%	12.22%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0111348696	G -> A	LOC_Os01g19970.1	upstream_gene_variant ; 1811.0bp to feature; MODIFIER	silent_mutation	Average:50.716; most accessible tissue: Minghui63 young leaf, score: 72.959	N	N	N	N
vg0111348696	G -> A	LOC_Os01g19960-LOC_Os01g19970	intergenic_region ; MODIFIER	silent_mutation	Average:50.716; most accessible tissue: Minghui63 young leaf, score: 72.959	N	N	N	N
vg0111348696	G -> DEL	N	N	silent_mutation	Average:50.716; most accessible tissue: Minghui63 young leaf, score: 72.959	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0111348696	NA	5.07E-24	mr1383	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
vg0111348696	1.80E-07	1.80E-07	mr1542_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