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Detailed information for vg1111156033:

Variant ID: vg1111156033 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 11156033
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, A: 0.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

GGCTCATGTCACAAGACAAAAAGTGGGTTCAAGAACTCCCATCAGTACTATGGGCCGTACGCACCACACCGACAACGTCCAATAAGGAAACACCATTCTT[C/A]
CTCGTGTACGGCTCCGAGGCCATGCTCCCCGGCGAGCTACGACATCAGAGTACACGAGTACAGAAGTATTCCGACGAGAACCAGGAGGAACAGTGAGACA

Reverse complement sequence

TGTCTCACTGTTCCTCCTGGTTCTCGTCGGAATACTTCTGTACTCGTGTACTCTGATGTCGTAGCTCGCCGGGGAGCATGGCCTCGGAGCCGTACACGAG[G/T]
AAGAATGGTGTTTCCTTATTGGACGTTGTCGGTGTGGTGCGTACGGCCCATAGTACTGATGGGAGTTCTTGAACCCACTTTTTGTCTTGTGACATGAGCC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.00%	13.90%	0.06%	0.00%	NA
All Indica	2759	78.70%	21.20%	0.11%	0.00%	NA
All Japonica	1512	99.60%	0.40%	0.00%	0.00%	NA
Aus	269	82.90%	17.10%	0.00%	0.00%	NA
Indica I	595	99.00%	1.00%	0.00%	0.00%	NA
Indica II	465	45.60%	54.20%	0.22%	0.00%	NA
Indica III	913	86.40%	13.40%	0.22%	0.00%	NA
Indica Intermediate	786	74.00%	26.00%	0.00%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	75.60%	24.40%	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
vg1111156033	C -> A	LOC_Os11g19390.1	missense_variant ; p.Phe394Leu; MODERATE	nonsynonymous_codon ; F394L	Average:50.67; most accessible tissue: Minghui63 young leaf, score: 70.655	possibly damaging	1.576	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1111156033	NA	9.28E-06	mr1044	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
vg1111156033	NA	2.75E-07	mr1277	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
vg1111156033	NA	1.47E-06	mr1352	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
vg1111156033	NA	3.91E-07	mr1609	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
vg1111156033	NA	1.61E-08	mr1829	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
vg1111156033	NA	1.96E-13	mr1829	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
vg1111156033	NA	1.70E-09	mr1842	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
vg1111156033	NA	1.81E-10	mr1902	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
vg1111156033	NA	9.25E-06	mr1050_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
vg1111156033	NA	1.68E-07	mr1167_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
vg1111156033	NA	7.91E-11	mr1794_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
vg1111156033	NA	1.29E-10	mr1829_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
vg1111156033	NA	5.99E-07	mr1842_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
vg1111156033	NA	5.03E-10	mr1902_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
vg1111156033	NA	4.58E-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