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Detailed information for vg1110764535:

Variant ID: vg1110764535 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10764535
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

AACACCAACCGAGACTAAAGTTAGGATCTTTAGTCCCGGTTGGTAACACCAACCATGCCCGCTGTAGCCACCAACCGGGACTAAAGATCATCTTTAGTCC[C/T]
GGTTTTTAGTGGAACCGGGACTATTGTGGATTTTGGCCGATCGACCAAAGATGGTTTCTCCACCAGTGGTAGTTGAAATCAACGTCAGTGTTCGTGACAC

Reverse complement sequence

GTGTCACGAACACTGACGTTGATTTCAACTACCACTGGTGGAGAAACCATCTTTGGTCGATCGGCCAAAATCCACAATAGTCCCGGTTCCACTAAAAACC[G/A]
GGACTAAAGATGATCTTTAGTCCCGGTTGGTGGCTACAGCGGGCATGGTTGGTGTTACCAACCGGGACTAAAGATCCTAACTTTAGTCTCGGTTGGTGTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.40%	9.30%	0.23%	0.00%	NA
All Indica	2759	84.50%	15.30%	0.25%	0.00%	NA
All Japonica	1512	99.20%	0.70%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	73.80%	26.20%	0.00%	0.00%	NA
Indica II	465	97.20%	2.60%	0.22%	0.00%	NA
Indica III	913	82.10%	17.70%	0.11%	0.00%	NA
Indica Intermediate	786	87.80%	11.60%	0.64%	0.00%	NA
Temperate Japonica	767	99.30%	0.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	1.20%	0.83%	0.00%	NA
VI/Aromatic	96	95.80%	2.10%	2.08%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg1110764535	C -> T	LOC_Os11g18930.1	downstream_gene_variant ; 588.0bp to feature; MODIFIER	silent_mutation	Average:60.944; most accessible tissue: Zhenshan97 flag leaf, score: 94.708	N	N	N	N
vg1110764535	C -> T	LOC_Os11g18919-LOC_Os11g18930	intergenic_region ; MODIFIER	silent_mutation	Average:60.944; most accessible tissue: Zhenshan97 flag leaf, score: 94.708	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110764535	2.17E-07	NA	Grain_thickness	Ind_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1110764535	NA	5.01E-09	mr1739	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
vg1110764535	NA	3.41E-08	mr1739	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
vg1110764535	NA	1.81E-07	mr1839	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
vg1110764535	NA	1.03E-08	mr1627_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