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Detailed information for vg1110845401:

Variant ID: vg1110845401 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10845401
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTTTAGAGATCGCCCCTCTTCTCGCTGATTCAGTTCTCGGAGATCGTCGGCACCACGAAGTTTCTCCCCAGTGATTCCCTTCCCACAAAGTTGGCCGGC[G/A]
GGTACCAGCAATATCACCCTCCACACATTCCTCTTCCTCATCCCATATCTTTATCCCCCGCCGCTTGAGTTTGCCTCCTCACCCCTATTGCTGGGCCAAC

Reverse complement sequence

GTTGGCCCAGCAATAGGGGTGAGGAGGCAAACTCAAGCGGCGGGGGATAAAGATATGGGATGAGGAAGAGGAATGTGTGGAGGGTGATATTGCTGGTACC[C/T]
GCCGGCCAACTTTGTGGGAAGGGAATCACTGGGGAGAAACTTCGTGGTGCCGACGATCTCCGAGAACTGAATCAGCGAGAAGAGGGGCGATCTCTAAAAC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.40%	13.00%	1.63%	0.00%	NA
All Indica	2759	98.30%	1.10%	0.54%	0.00%	NA
All Japonica	1512	57.70%	38.20%	4.10%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.30%	1.00%	0.67%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	95.70%	2.90%	1.40%	0.00%	NA
Temperate Japonica	767	32.70%	62.10%	5.22%	0.00%	NA
Tropical Japonica	504	92.90%	5.20%	1.98%	0.00%	NA
Japonica Intermediate	241	63.90%	31.10%	4.98%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg1110845401	G -> A	LOC_Os11g19030.1	upstream_gene_variant ; 132.0bp to feature; MODIFIER	silent_mutation	Average:50.393; most accessible tissue: Zhenshan97 young leaf, score: 71.923	N	N	N	N
vg1110845401	G -> A	LOC_Os11g19020.1	downstream_gene_variant ; 4061.0bp to feature; MODIFIER	silent_mutation	Average:50.393; most accessible tissue: Zhenshan97 young leaf, score: 71.923	N	N	N	N
vg1110845401	G -> A	LOC_Os11g19020-LOC_Os11g19030	intergenic_region ; MODIFIER	silent_mutation	Average:50.393; most accessible tissue: Zhenshan97 young leaf, score: 71.923	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110845401	2.54E-07	4.68E-09	mr1593	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
vg1110845401	1.21E-06	NA	mr1593	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