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Detailed information for vg1220351136:

Variant ID: vg1220351136 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 20351136
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCACACCCATGCTGCACAGGCCCAACCATCCTGAACAACCATACCCAGCTATACAGATCTATCTCCAAACCAGGAATGTACCATTCCAAACCAGGAGCTA[G/A]
TCAAATTATTACCAGTTATAGCATCATTTATTATGGTGAGAAGTGTGAGACTAATCATGAAAGACATTGTTAGACCCGCCCATAACCACTGGCATGGCTA

Reverse complement sequence

TAGCCATGCCAGTGGTTATGGGCGGGTCTAACAATGTCTTTCATGATTAGTCTCACACTTCTCACCATAATAAATGATGCTATAACTGGTAATAATTTGA[C/T]
TAGCTCCTGGTTTGGAATGGTACATTCCTGGTTTGGAGATAGATCTGTATAGCTGGGTATGGTTGTTCAGGATGGTTGGGCCTGTGCAGCATGGGTGTGC

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	31.70%	2.00%	2.60%	63.73%	NA
All Indica	2759	15.20%	0.90%	3.01%	80.90%	NA
All Japonica	1512	64.80%	3.60%	0.46%	31.08%	NA
Aus	269	17.50%	4.10%	11.15%	67.29%	NA
Indica I	595	37.50%	0.50%	2.35%	59.66%	NA
Indica II	465	13.30%	0.20%	0.86%	85.59%	NA
Indica III	913	1.50%	1.60%	4.16%	92.66%	NA
Indica Intermediate	786	15.10%	0.90%	3.44%	80.53%	NA
Temperate Japonica	767	91.50%	2.90%	0.00%	5.61%	NA
Tropical Japonica	504	29.60%	0.20%	1.39%	68.85%	NA
Japonica Intermediate	241	53.50%	13.30%	0.00%	33.20%	NA
VI/Aromatic	96	10.40%	1.00%	1.04%	87.50%	NA
Intermediate	90	45.60%	2.20%	2.22%	50.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1220351136	G -> DEL	N	N	silent_mutation	Average:7.91; most accessible tissue: Zhenshan97 young leaf, score: 17.571	N	N	N	N
vg1220351136	G -> A	LOC_Os12g33710.1	upstream_gene_variant ; 2416.0bp to feature; MODIFIER	silent_mutation	Average:7.91; most accessible tissue: Zhenshan97 young leaf, score: 17.571	N	N	N	N
vg1220351136	G -> A	LOC_Os12g33720.1	upstream_gene_variant ; 1448.0bp to feature; MODIFIER	silent_mutation	Average:7.91; most accessible tissue: Zhenshan97 young leaf, score: 17.571	N	N	N	N
vg1220351136	G -> A	LOC_Os12g33730.1	upstream_gene_variant ; 4471.0bp to feature; MODIFIER	silent_mutation	Average:7.91; most accessible tissue: Zhenshan97 young leaf, score: 17.571	N	N	N	N
vg1220351136	G -> A	LOC_Os12g33700.1	downstream_gene_variant ; 4829.0bp to feature; MODIFIER	silent_mutation	Average:7.91; most accessible tissue: Zhenshan97 young leaf, score: 17.571	N	N	N	N
vg1220351136	G -> A	LOC_Os12g33720-LOC_Os12g33730	intergenic_region ; MODIFIER	silent_mutation	Average:7.91; most accessible tissue: Zhenshan97 young leaf, score: 17.571	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1220351136	4.69E-08	4.69E-08	mr1191_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