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Detailed information for vg0813669113:

Variant ID: vg0813669113 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 13669113
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTACCTAGCACAGGAGACCAGGAAAGCTAATATGAGACAGTTAGTGGCAAGTTGTCAATCATGGTATCCTTGGTAAGTGGGATATCATAGTCGAAAGCAT[T/A]
TGGTGGTAAGCTGGAAGGAAACGCCAAGCATGGTATTCTCATGATGACAAGCATGGTATCCTAGTAATGACAAGCAGGTGTCGACACAAGACATGAAGTT

Reverse complement sequence

AACTTCATGTCTTGTGTCGACACCTGCTTGTCATTACTAGGATACCATGCTTGTCATCATGAGAATACCATGCTTGGCGTTTCCTTCCAGCTTACCACCA[A/T]
ATGCTTTCGACTATGATATCCCACTTACCAAGGATACCATGATTGACAACTTGCCACTAACTGTCTCATATTAGCTTTCCTGGTCTCCTGTGCTAGGTAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.90%	1.30%	16.99%	4.80%	NA
All Indica	2759	71.30%	1.90%	20.37%	6.42%	NA
All Japonica	1512	93.80%	0.00%	3.24%	2.91%	NA
Aus	269	32.00%	1.90%	65.80%	0.37%	NA
Indica I	595	58.70%	2.40%	30.92%	8.07%	NA
Indica II	465	79.80%	1.30%	13.33%	5.59%	NA
Indica III	913	75.70%	1.90%	18.40%	4.05%	NA
Indica Intermediate	786	70.70%	2.00%	18.83%	8.40%	NA
Temperate Japonica	767	92.60%	0.00%	2.61%	4.82%	NA
Tropical Japonica	504	96.40%	0.00%	3.17%	0.40%	NA
Japonica Intermediate	241	92.50%	0.00%	5.39%	2.07%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	76.70%	2.20%	15.56%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0813669113	T -> A	LOC_Os08g22740.1	intron_variant ; MODIFIER	silent_mutation	Average:22.288; most accessible tissue: Minghui63 root, score: 40.262	N	N	N	N
vg0813669113	T -> DEL	N	N	silent_mutation	Average:22.288; most accessible tissue: Minghui63 root, score: 40.262	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0813669113	2.37E-06	NA	mr1161_2	Ind_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