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Detailed information for vg0816229266:

Variant ID: vg0816229266 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16229266
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACGGACCCACTTAGAGATTTACTGTAATCTCAGTGCGTCTCACTTAGAGATAAAGTTGCTTTAATCTCAGTGTGTTTGAGACATTATATTGATATCCTA[T/G]
AGTTTGTCAAAACAATATTGGTTGTAATAAGTAGATAAGTACAAACTCCCTTATATTATAAGGTTATAAGACTTGCTAGTCATTAGAGTATGTATTATTA

Reverse complement sequence

TAATAATACATACTCTAATGACTAGCAAGTCTTATAACCTTATAATATAAGGGAGTTTGTACTTATCTACTTATTACAACCAATATTGTTTTGACAAACT[A/C]
TAGGATATCAATATAATGTCTCAAACACACTGAGATTAAAGCAACTTTATCTCTAAGTGAGACGCACTGAGATTACAGTAAATCTCTAAGTGGGTCCGTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.30%	4.60%	0.53%	5.59%	NA
All Indica	2759	99.40%	0.40%	0.07%	0.11%	NA
All Japonica	1512	67.90%	13.60%	1.32%	17.20%	NA
Aus	269	98.90%	0.00%	1.12%	0.00%	NA
Indica I	595	98.70%	1.20%	0.17%	0.00%	NA
Indica II	465	99.60%	0.20%	0.22%	0.00%	NA
Indica III	913	99.80%	0.00%	0.00%	0.22%	NA
Indica Intermediate	786	99.50%	0.40%	0.00%	0.13%	NA
Temperate Japonica	767	75.90%	23.10%	0.13%	0.91%	NA
Tropical Japonica	504	48.20%	4.20%	3.37%	44.25%	NA
Japonica Intermediate	241	83.40%	3.30%	0.83%	12.45%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	97.80%	2.20%	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
vg0816229266	T -> G	LOC_Os08g26690.1	intron_variant ; MODIFIER	silent_mutation	Average:9.588; most accessible tissue: Callus, score: 32.155	N	N	N	N
vg0816229266	T -> DEL	N	N	silent_mutation	Average:9.588; most accessible tissue: Callus, score: 32.155	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816229266	2.51E-06	8.88E-06	mr1440_2	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
vg0816229266	3.31E-06	3.31E-06	mr1440_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251