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Detailed information for vg1127570270:

Variant ID: vg1127570270 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27570270
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCAATTTCCCGGCAACTGCGTAATTGGTTTTTTATCTATATTTAATACTTCATATATGTGTTTAAATATTCGATGTGACAATATGAAAAAATTTGTTTGG[G/A]
AACTAAATAGGCCCTAAGCCAAATTGGCCAGATGTGATCGATCGTTCAAATGGGCAATTATGTTTGCTAGGCAAACCATGTGGCCGGAGGCCATGCATGT

Reverse complement sequence

ACATGCATGGCCTCCGGCCACATGGTTTGCCTAGCAAACATAATTGCCCATTTGAACGATCGATCACATCTGGCCAATTTGGCTTAGGGCCTATTTAGTT[C/T]
CCAAACAAATTTTTTCATATTGTCACATCGAATATTTAAACACATATATGAAGTATTAAATATAGATAAAAAACCAATTACGCAGTTGCCGGGAAATTGC

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	45.70%	1.10%	1.21%	51.93%	NA
All Indica	2759	46.60%	0.70%	0.76%	51.98%	NA
All Japonica	1512	47.10%	2.30%	0.60%	50.00%	NA
Aus	269	16.70%	0.00%	9.29%	73.98%	NA
Indica I	595	66.60%	2.70%	0.50%	30.25%	NA
Indica II	465	84.10%	0.00%	0.00%	15.91%	NA
Indica III	913	13.50%	0.10%	0.99%	85.43%	NA
Indica Intermediate	786	47.70%	0.30%	1.15%	50.89%	NA
Temperate Japonica	767	61.00%	3.00%	0.91%	35.07%	NA
Tropical Japonica	504	27.60%	0.60%	0.20%	71.63%	NA
Japonica Intermediate	241	43.60%	3.70%	0.41%	52.28%	NA
VI/Aromatic	96	66.70%	0.00%	0.00%	33.33%	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
vg1127570270	G -> A	LOC_Os11g45530.1	upstream_gene_variant ; 2807.0bp to feature; MODIFIER	silent_mutation	Average:32.993; most accessible tissue: Callus, score: 62.298	N	N	N	N
vg1127570270	G -> A	LOC_Os11g45540.1	downstream_gene_variant ; 813.0bp to feature; MODIFIER	silent_mutation	Average:32.993; most accessible tissue: Callus, score: 62.298	N	N	N	N
vg1127570270	G -> A	LOC_Os11g45550.1	downstream_gene_variant ; 4769.0bp to feature; MODIFIER	silent_mutation	Average:32.993; most accessible tissue: Callus, score: 62.298	N	N	N	N
vg1127570270	G -> A	LOC_Os11g45530-LOC_Os11g45540	intergenic_region ; MODIFIER	silent_mutation	Average:32.993; most accessible tissue: Callus, score: 62.298	N	N	N	N
vg1127570270	G -> DEL	N	N	silent_mutation	Average:32.993; most accessible tissue: Callus, score: 62.298	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127570270	3.36E-06	3.36E-06	mr1430_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