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Detailed information for vg1124274881:

Variant ID: vg1124274881 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24274881
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCGATGCAAGCGGCCAGTACTCCGCCGCCGCCGGCCGTAGCCGATGCCGCCGCGGGGAGACGATGGGGGAGGGGCGCCGGGGCAAGGCCACTCGAAGGC[G/A]
GCGCACTCCCCCTTGGGCGAGTGCGCGCACCGGCGAGGGGGCATGCGCCGGCGCCGCCTATGAGCGCCATAGCTCCGCCGTGAGAGAGGGAAGGGAGGAG

Reverse complement sequence

CTCCTCCCTTCCCTCTCTCACGGCGGAGCTATGGCGCTCATAGGCGGCGCCGGCGCATGCCCCCTCGCCGGTGCGCGCACTCGCCCAAGGGGGAGTGCGC[C/T]
GCCTTCGAGTGGCCTTGCCCCGGCGCCCCTCCCCCATCGTCTCCCCGCGGCGGCATCGGCTACGGCCGGCGGCGGCGGAGTACTGGCCGCTTGCATCGGC

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	95.90%	3.10%	0.95%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	87.60%	9.50%	2.98%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	96.70%	2.10%	1.17%	0.00%	NA
Tropical Japonica	504	70.80%	22.20%	6.94%	0.00%	NA
Japonica Intermediate	241	93.40%	6.20%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg1124274881	G -> A	LOC_Os11g40674.1	downstream_gene_variant ; 626.0bp to feature; MODIFIER	silent_mutation	Average:69.957; most accessible tissue: Zhenshan97 young leaf, score: 85.184	N	N	N	N
vg1124274881	G -> A	LOC_Os11g40680.1	downstream_gene_variant ; 3741.0bp to feature; MODIFIER	silent_mutation	Average:69.957; most accessible tissue: Zhenshan97 young leaf, score: 85.184	N	N	N	N
vg1124274881	G -> A	LOC_Os11g40674-LOC_Os11g40680	intergenic_region ; MODIFIER	silent_mutation	Average:69.957; most accessible tissue: Zhenshan97 young leaf, score: 85.184	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124274881	4.52E-06	5.55E-06	mr1218	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