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Detailed information for vg1128476692:

Variant ID: vg1128476692 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 28476692
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.82, T: 0.19, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:

GAGTTCTCAGTTCTACAGAAGGCTTTATCCATGACTTGGATGAGAAGGTATCCACATCTCAAATTACACGTTTCACATTTCAAGCCTCCTCCCCAATCTT[A/T]
TTTAAGTATGAGTTGCCTGTATAATATCATCAGTAGGTTTGCACATGAATTCAGATAGGAGTGCTGGCAGTCTGGCTCAGTACTATATGTTTTTTTGAAT

Reverse complement sequence

ATTCAAAAAAACATATAGTACTGAGCCAGACTGCCAGCACTCCTATCTGAATTCATGTGCAAACCTACTGATGATATTATACAGGCAACTCATACTTAAA[T/A]
AAGATTGGGGAGGAGGCTTGAAATGTGAAACGTGTAATTTGAGATGTGGATACCTTCTCATCCAAGTCATGGATAAAGCCTTCTGTAGAACTGAGAACTC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.10%	22.30%	3.30%	18.30%	NA
All Indica	2759	43.80%	34.80%	3.66%	17.80%	NA
All Japonica	1512	79.60%	1.60%	1.98%	16.87%	NA
Aus	269	64.70%	15.20%	2.97%	17.10%	NA
Indica I	595	44.50%	32.90%	2.69%	19.83%	NA
Indica II	465	14.60%	65.80%	2.80%	16.77%	NA
Indica III	913	54.90%	21.10%	5.70%	18.29%	NA
Indica Intermediate	786	47.60%	33.60%	2.54%	16.28%	NA
Temperate Japonica	767	82.70%	1.70%	1.96%	13.69%	NA
Tropical Japonica	504	72.80%	1.40%	2.38%	23.41%	NA
Japonica Intermediate	241	83.80%	1.70%	1.24%	13.28%	NA
VI/Aromatic	96	13.50%	17.70%	16.67%	52.08%	NA
Intermediate	90	58.90%	14.40%	1.11%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1128476692	A -> T	LOC_Os11g47330.1	intron_variant ; MODIFIER	silent_mutation	Average:24.699; most accessible tissue: Zhenshan97 flower, score: 68.372	N	N	N	N
vg1128476692	A -> DEL	N	N	silent_mutation	Average:24.699; most accessible tissue: Zhenshan97 flower, score: 68.372	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1128476692	3.58E-07	3.44E-07	mr1662	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
vg1128476692	NA	8.38E-08	mr1662_2	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