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Detailed information for vg1116343038:

Variant ID: vg1116343038 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 16343038
Reference Allele: T	Alternative Allele: A,TGTTGGGATACGCGTA,TGTTG,TGTTGGGATATGCGTA,TCACTAACACTATAA
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTTTCTCTACACTAACTTTTAGGTAATGCTATTTCTTTCTACTCTCACGAAGCTAGCTACATCACCTTATTGTTTTAGTCTTTGGATCATTCATCTATA[T/A,TGTTGGGATACGCGTA,TGTTG,TGTTGGGATATGCGTA,TCACTAACACTATAA]
GGCATAGATCGTTTCGTTCTACTTATCTCATGGAGCCATGTGTATCATCTCGTCAACCATTTTTTTACCACATGAAAACCATGATCTTCATTTTTGGCCT

Reverse complement sequence

AGGCCAAAAATGAAGATCATGGTTTTCATGTGGTAAAAAAATGGTTGACGAGATGATACACATGGCTCCATGAGATAAGTAGAACGAAACGATCTATGCC[A/T,TACGCGTATCCCAACA,CAACA,TACGCATATCCCAACA,TTATAGTGTTAGTGA]
TATAGATGAATGATCCAAAGACTAAAACAATAAGGTGATGTAGCTAGCTTCGTGAGAGTAGAAAGAAATAGCATTACCTAAAAGTTAGTGTAGAGAAACT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.80%	4.90%	29.67%	0.74%	TGTTGGGATACGCGTA: 0.40%; TGTTGGGATATGCGTA: 0.30%; TGTTG: 0.19%
All Indica	2759	57.80%	6.70%	34.00%	0.40%	TGTTGGGATATGCGTA: 0.51%; TGTTGGGATACGCGTA: 0.29%; TGTTG: 0.22%
All Japonica	1512	74.90%	1.80%	21.10%	1.52%	TGTTGGGATACGCGTA: 0.53%; TGTTG: 0.20%
Aus	269	49.80%	5.60%	43.12%	0.37%	TGTTGGGATACGCGTA: 1.12%
Indica I	595	57.60%	2.90%	37.65%	0.67%	TGTTGGGATATGCGTA: 0.67%; TGTTGGGATACGCGTA: 0.34%; TGTTG: 0.17%
Indica II	465	57.00%	7.10%	34.84%	0.43%	TGTTGGGATATGCGTA: 0.43%; TGTTG: 0.22%
Indica III	913	60.00%	10.10%	28.70%	0.22%	TGTTGGGATATGCGTA: 0.55%; TGTTGGGATACGCGTA: 0.33%; TGTTG: 0.11%
Indica Intermediate	786	56.00%	5.60%	36.90%	0.38%	TGTTG: 0.38%; TGTTGGGATATGCGTA: 0.38%; TGTTGGGATACGCGTA: 0.38%
Temperate Japonica	767	89.60%	0.70%	9.65%	0.13%	NA
Tropical Japonica	504	61.30%	3.00%	30.56%	3.37%	TGTTGGGATACGCGTA: 1.39%; TGTTG: 0.40%
Japonica Intermediate	241	56.40%	2.90%	37.76%	2.07%	TGTTGGGATACGCGTA: 0.41%; TGTTG: 0.41%
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	64.40%	4.40%	31.11%	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
vg1116343038	T -> A	LOC_Os11g28380.1	upstream_gene_variant ; 2456.0bp to feature; MODIFIER	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> A	LOC_Os11g28400.1	upstream_gene_variant ; 874.0bp to feature; MODIFIER	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> A	LOC_Os11g28370.1	downstream_gene_variant ; 4499.0bp to feature; MODIFIER	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> A	LOC_Os11g28390.1	downstream_gene_variant ; 259.0bp to feature; MODIFIER	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> A	LOC_Os11g28390-LOC_Os11g28400	intergenic_region ; MODIFIER	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> TGTTGGGATATGCGTA	LOC_Os11g28380.1	upstream_gene_variant ; 2457.0bp to feature; MODIFIER	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> TGTTGGGATATGCGTA	LOC_Os11g28400.1	upstream_gene_variant ; 873.0bp to feature; MODIFIER	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> TGTTGGGATATGCGTA	LOC_Os11g28370.1	downstream_gene_variant ; 4500.0bp to feature; MODIFIER	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> TGTTGGGATATGCGTA	LOC_Os11g28390.1	downstream_gene_variant ; 260.0bp to feature; MODIFIER	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> TGTTGGGATATGCGTA	LOC_Os11g28390-LOC_Os11g28400	intergenic_region ; MODIFIER	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> DEL	N	N	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> TGTTGGGATACGCGTA	LOC_Os11g28380.1	upstream_gene_variant ; 2457.0bp to feature; MODIFIER	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> TGTTGGGATACGCGTA	LOC_Os11g28400.1	upstream_gene_variant ; 873.0bp to feature; MODIFIER	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> TGTTGGGATACGCGTA	LOC_Os11g28370.1	downstream_gene_variant ; 4500.0bp to feature; MODIFIER	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> TGTTGGGATACGCGTA	LOC_Os11g28390.1	downstream_gene_variant ; 260.0bp to feature; MODIFIER	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> TGTTGGGATACGCGTA	LOC_Os11g28390-LOC_Os11g28400	intergenic_region ; MODIFIER	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> TGTTG	LOC_Os11g28380.1	upstream_gene_variant ; 2457.0bp to feature; MODIFIER	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> TGTTG	LOC_Os11g28400.1	upstream_gene_variant ; 873.0bp to feature; MODIFIER	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> TGTTG	LOC_Os11g28370.1	downstream_gene_variant ; 4500.0bp to feature; MODIFIER	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> TGTTG	LOC_Os11g28390.1	downstream_gene_variant ; 260.0bp to feature; MODIFIER	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> TGTTG	LOC_Os11g28390-LOC_Os11g28400	intergenic_region ; MODIFIER	silent_mutation	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> TCACTAACACTATAA	LOC_Os11g28380.1	upstream_gene_variant ; 2457.0bp to feature; MODIFIER	N	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> TCACTAACACTATAA	LOC_Os11g28400.1	upstream_gene_variant ; 873.0bp to feature; MODIFIER	N	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> TCACTAACACTATAA	LOC_Os11g28370.1	downstream_gene_variant ; 4500.0bp to feature; MODIFIER	N	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> TCACTAACACTATAA	LOC_Os11g28390.1	downstream_gene_variant ; 260.0bp to feature; MODIFIER	N	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N
vg1116343038	T -> TCACTAACACTATAA	LOC_Os11g28390-LOC_Os11g28400	intergenic_region ; MODIFIER	N	Average:46.539; most accessible tissue: Callus, score: 91.349	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116343038	1.31E-06	NA	mr1410	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