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Detailed information for vg1127516332:

Variant ID: vg1127516332 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27516332
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTTCCAAAATTGGTTGCAAAAACGGATTCCCCTCGATCTCCTCTATCTTATCCCCAAGAAATCCCCTTGAATCCCGTGGTATATCGCGTGGATTCGACG[T/C]
GGTTTTGAGTTCCTATTTTCCGGCGAACCCTAACTAATCCGTCGCCAATTCCATCCGTTCCTGAGCCGATCTCTCCCTCTTCCGGCTATAAATAGCAGTC

Reverse complement sequence

GACTGCTATTTATAGCCGGAAGAGGGAGAGATCGGCTCAGGAACGGATGGAATTGGCGACGGATTAGTTAGGGTTCGCCGGAAAATAGGAACTCAAAACC[A/G]
CGTCGAATCCACGCGATATACCACGGGATTCAAGGGGATTTCTTGGGGATAAGATAGAGGAGATCGAGGGGAATCCGTTTTTGCAACCAATTTTGGAAAC

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	80.20%	11.90%	4.49%	3.43%	NA
All Indica	2759	97.50%	2.00%	0.40%	0.14%	NA
All Japonica	1512	45.20%	31.90%	12.70%	10.19%	NA
Aus	269	93.70%	3.70%	1.49%	1.12%	NA
Indica I	595	97.80%	1.70%	0.50%	0.00%	NA
Indica II	465	96.10%	3.00%	0.86%	0.00%	NA
Indica III	913	99.10%	0.80%	0.11%	0.00%	NA
Indica Intermediate	786	96.10%	3.10%	0.38%	0.51%	NA
Temperate Japonica	767	21.30%	39.20%	21.38%	18.12%	NA
Tropical Japonica	504	74.40%	24.00%	1.19%	0.40%	NA
Japonica Intermediate	241	60.60%	24.90%	9.13%	5.39%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	75.60%	17.80%	5.56%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127516332	T -> DEL	N	N	silent_mutation	Average:29.946; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1127516332	T -> C	LOC_Os11g45440.1	upstream_gene_variant ; 2047.0bp to feature; MODIFIER	silent_mutation	Average:29.946; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1127516332	T -> C	LOC_Os11g45450.1	downstream_gene_variant ; 3107.0bp to feature; MODIFIER	silent_mutation	Average:29.946; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1127516332	T -> C	LOC_Os11g45440-LOC_Os11g45450	intergenic_region ; MODIFIER	silent_mutation	Average:29.946; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127516332	5.49E-08	1.56E-06	mr1805	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