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Detailed information for vg1122878285:

Variant ID: vg1122878285 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22878285
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

TGATAATTTGAAGAAAAACCTCTTGGAAGTCTGCACTTATGATTATCGTGAAATCATTTTACCAGCTATGAAAGATTTCCTATGGGTTAGTCTAGTTCTT[G/A]
TATGTTATTTGACTTTGATAAATAATACTACTTTGCTTATCATTGTTTTCATGGTTGCACTCATGCAGGCTAAACTGTGTAATGTTCCACCTAAAGGGGT

Reverse complement sequence

ACCCCTTTAGGTGGAACATTACACAGTTTAGCCTGCATGAGTGCAACCATGAAAACAATGATAAGCAAAGTAGTATTATTTATCAAAGTCAAATAACATA[C/T]
AAGAACTAGACTAACCCATAGGAAATCTTTCATAGCTGGTAAAATGATTTCACGATAATCATAAGTGCAGACTTCCAAGAGGTTTTTCTTCAAATTATCA

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	78.20%	21.70%	0.08%	0.00%	NA
All Indica	2759	71.80%	28.00%	0.14%	0.00%	NA
All Japonica	1512	84.50%	15.50%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	31.10%	68.70%	0.17%	0.00%	NA
Indica II	465	97.80%	2.20%	0.00%	0.00%	NA
Indica III	913	82.00%	17.70%	0.22%	0.00%	NA
Indica Intermediate	786	75.40%	24.40%	0.13%	0.00%	NA
Temperate Japonica	767	72.90%	27.10%	0.00%	0.00%	NA
Tropical Japonica	504	96.80%	3.20%	0.00%	0.00%	NA
Japonica Intermediate	241	95.90%	4.10%	0.00%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	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
vg1122878285	G -> A	LOC_Os11g38610.2	intron_variant ; MODIFIER	silent_mutation	Average:19.324; most accessible tissue: Callus, score: 26.353	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122878285	NA	8.13E-06	mr1074	Ind_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
vg1122878285	5.05E-06	NA	mr1336	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
vg1122878285	6.55E-06	NA	mr1336_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
vg1122878285	NA	9.44E-06	mr1923_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
vg1122878285	NA	1.27E-07	mr1933_2	Ind_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