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Detailed information for vg0511944956:

Variant ID: vg0511944956 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 11944956
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCAATCCCCGGACAGGAGTAGGGTATTACTTCTTGAATAAGAAGGCCTGAACCTGTATAAAATTCCTTGTCTCCAAACCCATCTACTTTTCCAGCTTGG[T/C]
AGCTACCCCCTTTTAGTATTGCCGAAATCTTGTTTCGACATGTATATATGTATATATATATATGTATATGTATATGTATATATATACATATATATGTATA

Reverse complement sequence

TATACATATATATGTATATATATACATATACATATACATATATATATATACATATATACATGTCGAAACAAGATTTCGGCAATACTAAAAGGGGGTAGCT[A/G]
CCAAGCTGGAAAAGTAGATGGGTTTGGAGACAAGGAATTTTATACAGGTTCAGGCCTTCTTATTCAAGAAGTAATACCCTACTCCTGTCCGGGGATTGAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.40%	1.90%	6.37%	5.40%	NA
All Indica	2759	89.60%	0.20%	5.80%	4.39%	NA
All Japonica	1512	91.00%	5.20%	3.57%	0.20%	NA
Aus	269	23.00%	0.00%	30.11%	46.84%	NA
Indica I	595	95.80%	0.70%	3.53%	0.00%	NA
Indica II	465	97.40%	0.00%	1.72%	0.86%	NA
Indica III	913	83.10%	0.10%	8.21%	8.54%	NA
Indica Intermediate	786	87.80%	0.10%	7.12%	4.96%	NA
Temperate Japonica	767	86.30%	8.00%	5.74%	0.00%	NA
Tropical Japonica	504	97.40%	1.00%	1.19%	0.40%	NA
Japonica Intermediate	241	92.50%	5.40%	1.66%	0.41%	NA
VI/Aromatic	96	96.90%	1.00%	1.04%	1.04%	NA
Intermediate	90	86.70%	3.30%	5.56%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0511944956	T -> DEL	N	N	silent_mutation	Average:43.259; most accessible tissue: Minghui63 young leaf, score: 65.92	N	N	N	N
vg0511944956	T -> C	LOC_Os05g20370.1	upstream_gene_variant ; 1425.0bp to feature; MODIFIER	silent_mutation	Average:43.259; most accessible tissue: Minghui63 young leaf, score: 65.92	N	N	N	N
vg0511944956	T -> C	LOC_Os05g20380.1	upstream_gene_variant ; 4798.0bp to feature; MODIFIER	silent_mutation	Average:43.259; most accessible tissue: Minghui63 young leaf, score: 65.92	N	N	N	N
vg0511944956	T -> C	LOC_Os05g20360.1	downstream_gene_variant ; 4663.0bp to feature; MODIFIER	silent_mutation	Average:43.259; most accessible tissue: Minghui63 young leaf, score: 65.92	N	N	N	N
vg0511944956	T -> C	LOC_Os05g20370-LOC_Os05g20380	intergenic_region ; MODIFIER	silent_mutation	Average:43.259; most accessible tissue: Minghui63 young leaf, score: 65.92	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0511944956	1.25E-06	4.78E-08	mr1648	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
vg0511944956	2.82E-07	7.83E-09	mr1697	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