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Detailed information for vg1105103677:

Variant ID: vg1105103677 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5103677
Reference Allele: A	Alternative Allele: T,G
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATGATTGATGATTGCTCTATCAGAAACCTGCAAGGTTTAAGGAGCAATCCATGCCTTGTTTTATCTGTAGAAAAACCATGTGGGGAAAACATGAGATAA[A/T,G]
GCATAAGCTTGTATCTATCATTGTCTCATTAAAAACTTTGTATGGGAAAAACGAGATGGTGAAAACTCACAAAAGGAAAAAGAGTACAATGTGAAGCGTT

Reverse complement sequence

AACGCTTCACATTGTACTCTTTTTCCTTTTGTGAGTTTTCACCATCTCGTTTTTCCCATACAAAGTTTTTAATGAGACAATGATAGATACAAGCTTATGC[T/A,C]
TTATCTCATGTTTTCCCCACATGGTTTTTCTACAGATAAAACAAGGCATGGATTGCTCCTTAAACCTTGCAGGTTTCTGATAGAGCAATCATCAATCATA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.90%	0.60%	0.55%	0.00%	NA
All Indica	2759	99.60%	0.20%	0.22%	0.00%	NA
All Japonica	1512	97.30%	1.40%	1.32%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.80%	0.00%	0.22%	0.00%	NA
Indica Intermediate	786	99.10%	0.40%	0.51%	0.00%	NA
Temperate Japonica	767	97.10%	1.00%	1.83%	0.00%	NA
Tropical Japonica	504	96.20%	2.60%	1.19%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	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
vg1105103677	A -> T	LOC_Os11g09510.1	upstream_gene_variant ; 3857.0bp to feature; MODIFIER	silent_mutation	Average:28.214; most accessible tissue: Callus, score: 42.037	N	N	N	N
vg1105103677	A -> T	LOC_Os11g09520.1	downstream_gene_variant ; 101.0bp to feature; MODIFIER	silent_mutation	Average:28.214; most accessible tissue: Callus, score: 42.037	N	N	N	N
vg1105103677	A -> T	LOC_Os11g09530.1	downstream_gene_variant ; 3230.0bp to feature; MODIFIER	silent_mutation	Average:28.214; most accessible tissue: Callus, score: 42.037	N	N	N	N
vg1105103677	A -> T	LOC_Os11g09510-LOC_Os11g09520	intergenic_region ; MODIFIER	silent_mutation	Average:28.214; most accessible tissue: Callus, score: 42.037	N	N	N	N
vg1105103677	A -> G	LOC_Os11g09510.1	upstream_gene_variant ; 3857.0bp to feature; MODIFIER	N	Average:28.214; most accessible tissue: Callus, score: 42.037	N	N	N	N
vg1105103677	A -> G	LOC_Os11g09520.1	downstream_gene_variant ; 101.0bp to feature; MODIFIER	N	Average:28.214; most accessible tissue: Callus, score: 42.037	N	N	N	N
vg1105103677	A -> G	LOC_Os11g09530.1	downstream_gene_variant ; 3230.0bp to feature; MODIFIER	N	Average:28.214; most accessible tissue: Callus, score: 42.037	N	N	N	N
vg1105103677	A -> G	LOC_Os11g09510-LOC_Os11g09520	intergenic_region ; MODIFIER	N	Average:28.214; most accessible tissue: Callus, score: 42.037	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105103677	4.51E-06	NA	mr1713_2	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