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Detailed information for vg1119998277:

Variant ID: vg1119998277 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19998277
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAATAAAGATATACATTGAAACATGTGAATTATGTTGGATGATAATTTAATATGTTTGTATTTGAAAAGCTCTTAAATTATAAAAACTATAAAGATATAA[C/T]
ATGTTTGTATGATGTTTAAATGTGATGATTGTTAGTGGATGATGATGTGGCATCTTGTTAATTAGTGGATTAGTGGATGATGATGTGACATCTTTGCATG

Reverse complement sequence

CATGCAAAGATGTCACATCATCATCCACTAATCCACTAATTAACAAGATGCCACATCATCATCCACTAACAATCATCACATTTAAACATCATACAAACAT[G/A]
TTATATCTTTATAGTTTTTATAATTTAAGAGCTTTTCAAATACAAACATATTAAATTATCATCCAACATAATTCACATGTTTCAATGTATATCTTTATTA

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	95.50%	4.40%	0.08%	0.00%	NA
All Indica	2759	93.70%	6.20%	0.14%	0.00%	NA
All Japonica	1512	98.90%	1.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	73.40%	25.90%	0.67%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	98.30%	1.70%	0.00%	0.00%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	95.90%	4.10%	0.00%	0.00%	NA
VI/Aromatic	96	78.10%	21.90%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg1119998277	C -> T	LOC_Os11g34150.1	upstream_gene_variant ; 1304.0bp to feature; MODIFIER	silent_mutation	Average:29.26; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg1119998277	C -> T	LOC_Os11g34150.2	upstream_gene_variant ; 1304.0bp to feature; MODIFIER	silent_mutation	Average:29.26; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg1119998277	C -> T	LOC_Os11g34150.3	upstream_gene_variant ; 1304.0bp to feature; MODIFIER	silent_mutation	Average:29.26; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg1119998277	C -> T	LOC_Os11g34160.1	downstream_gene_variant ; 3729.0bp to feature; MODIFIER	silent_mutation	Average:29.26; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg1119998277	C -> T	LOC_Os11g34150-LOC_Os11g34160	intergenic_region ; MODIFIER	silent_mutation	Average:29.26; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119998277	4.83E-06	NA	mr1585_2	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