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Detailed information for vg1111482820:

Variant ID: vg1111482820 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 11482820
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:

TGATATGGGATTATATGATGGAAATCACAGATTACAAAGGGAACAGTGGAACTCGATGATACCGACGAGACCGTAGTCGAGTTGGTTCGACTAGATCACC[C/T]
GGCGACTTGGCTCCTGTAGGCTCCGGCTTCGTAGGCTATGGTGGTTGTCTCGGCGGTGAGATTCGATGCCTTAGGTCCTCCCGGGGGTCCCTTTTATACC

Reverse complement sequence

GGTATAAAAGGGACCCCCGGGAGGACCTAAGGCATCGAATCTCACCGCCGAGACAACCACCATAGCCTACGAAGCCGGAGCCTACAGGAGCCAAGTCGCC[G/A]
GGTGATCTAGTCGAACCAACTCGACTACGGTCTCGTCGGTATCATCGAGTTCCACTGTTCCCTTTGTAATCTGTGATTTCCATCATATAATCCCATATCA

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	98.30%	0.90%	0.74%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.04%	0.00%	NA
All Japonica	1512	95.00%	2.80%	2.25%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	91.10%	5.20%	3.65%	0.00%	NA
Tropical Japonica	504	99.40%	0.20%	0.40%	0.00%	NA
Japonica Intermediate	241	97.90%	0.40%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg1111482820	C -> T	LOC_Os11g19950.1	upstream_gene_variant ; 245.0bp to feature; MODIFIER	silent_mutation	Average:58.785; most accessible tissue: Minghui63 young leaf, score: 78.821	N	N	N	N
vg1111482820	C -> T	LOC_Os11g19960.1	upstream_gene_variant ; 4932.0bp to feature; MODIFIER	silent_mutation	Average:58.785; most accessible tissue: Minghui63 young leaf, score: 78.821	N	N	N	N
vg1111482820	C -> T	LOC_Os11g19950-LOC_Os11g19960	intergenic_region ; MODIFIER	silent_mutation	Average:58.785; most accessible tissue: Minghui63 young leaf, score: 78.821	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1111482820	3.06E-06	2.07E-08	mr1062	Jap_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
vg1111482820	7.39E-06	1.46E-07	mr1062_2	Jap_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