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Detailed information for vg1100929952:

Variant ID: vg1100929952 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 929952
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, T: 0.11, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

CTCCGACCGGACGAGACGCACTGCCTCATCCGTGTCGTTTGAGAAGCACTCACTTAGTTGTTTCAAAAAGGAGTTTAAATAAAATCAATTGCAAAAACAA[T/C]
AGCCTTTCCTTTGAAGCCTGCATTAAACACTTAATTCCCATGGCTTACTGAGTACTCATGTACTCACCCTTGCTCTATATAAATAATCCCCCTCCCCGCA

Reverse complement sequence

TGCGGGGAGGGGGATTATTTATATAGAGCAAGGGTGAGTACATGAGTACTCAGTAAGCCATGGGAATTAAGTGTTTAATGCAGGCTTCAAAGGAAAGGCT[A/G]
TTGTTTTTGCAATTGATTTTATTTAAACTCCTTTTTGAAACAACTAAGTGAGTGCTTCTCAAACGACACGGATGAGGCAGTGCGTCTCGTCCGGTCGGAG

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	58.90%	27.80%	8.84%	4.49%	NA
All Indica	2759	93.00%	4.30%	2.54%	0.18%	NA
All Japonica	1512	2.20%	62.60%	21.69%	13.49%	NA
Aus	269	53.20%	46.50%	0.37%	0.00%	NA
Indica I	595	96.10%	2.20%	1.68%	0.00%	NA
Indica II	465	84.90%	7.70%	6.88%	0.43%	NA
Indica III	913	95.90%	3.40%	0.66%	0.00%	NA
Indica Intermediate	786	92.00%	4.80%	2.80%	0.38%	NA
Temperate Japonica	767	2.50%	63.20%	23.86%	10.43%	NA
Tropical Japonica	504	1.20%	63.30%	17.86%	17.66%	NA
Japonica Intermediate	241	3.30%	59.30%	22.82%	14.52%	NA
VI/Aromatic	96	11.50%	86.50%	2.08%	0.00%	NA
Intermediate	90	33.30%	44.40%	18.89%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1100929952	T -> DEL	N	N	silent_mutation	Average:52.25; most accessible tissue: Zhenshan97 flower, score: 75.657	N	N	N	N
vg1100929952	T -> C	LOC_Os11g02780.1	upstream_gene_variant ; 2875.0bp to feature; MODIFIER	silent_mutation	Average:52.25; most accessible tissue: Zhenshan97 flower, score: 75.657	N	N	N	N
vg1100929952	T -> C	LOC_Os11g02790.1	downstream_gene_variant ; 1355.0bp to feature; MODIFIER	silent_mutation	Average:52.25; most accessible tissue: Zhenshan97 flower, score: 75.657	N	N	N	N
vg1100929952	T -> C	LOC_Os11g02800.1	downstream_gene_variant ; 1405.0bp to feature; MODIFIER	silent_mutation	Average:52.25; most accessible tissue: Zhenshan97 flower, score: 75.657	N	N	N	N
vg1100929952	T -> C	LOC_Os11g02790-LOC_Os11g02800	intergenic_region ; MODIFIER	silent_mutation	Average:52.25; most accessible tissue: Zhenshan97 flower, score: 75.657	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1100929952	2.68E-06	NA	mr1529	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