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Detailed information for vg1120148591:

Variant ID: vg1120148591 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 20148591
Reference Allele: C	Alternative Allele: T,CTGTTTACGAAAAACACGA
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACCTCAACCACGTGGATTGGGCACAGATGGACTGCGTCGTCCTCGGCTAGCTATAAGGCACGATCTCCGCCGACTTGCTTCAGGAAGTCATGTTGGCCA[C/T,CTGTTTACGAAAAACACGA]
GGCTACGGCTCGCTCTGTTTGGTGTGATCTCGCCCATCAATTCCTCGGCAACCAAGAATGTTGCACCATCAATGTCAACGCCGAGTTCCGCAACTTCTCT

Reverse complement sequence

AGAGAAGTTGCGGAACTCGGCGTTGACATTGATGGTGCAACATTCTTGGTTGCCGAGGAATTGATGGGCGAGATCACACCAAACAGAGCGAGCCGTAGCC[G/A,TCGTGTTTTTCGTAAACAG]
TGGCCAACATGACTTCCTGAAGCAAGTCGGCGGAGATCGTGCCTTATAGCTAGCCGAGGACGACGCAGTCCATCTGTGCCCAATCCACGTGGTTGAGGTG

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	60.50%	3.90%	35.12%	0.40%	CTGTTTACGAAAAACACGA: 0.13%
All Indica	2759	55.40%	4.50%	39.40%	0.62%	CTGTTTACGAAAAACACGA: 0.14%
All Japonica	1512	74.20%	2.30%	23.28%	0.07%	CTGTTTACGAAAAACACGA: 0.13%
Aus	269	24.50%	8.90%	66.54%	0.00%	NA
Indica I	595	49.40%	3.70%	46.39%	0.50%	NA
Indica II	465	56.10%	3.70%	39.78%	0.22%	CTGTTTACGAAAAACACGA: 0.22%
Indica III	913	63.30%	5.10%	30.56%	0.88%	CTGTTTACGAAAAACACGA: 0.11%
Indica Intermediate	786	50.30%	4.70%	44.15%	0.64%	CTGTTTACGAAAAACACGA: 0.25%
Temperate Japonica	767	85.30%	1.40%	13.30%	0.00%	NA
Tropical Japonica	504	68.80%	3.40%	27.38%	0.20%	CTGTTTACGAAAAACACGA: 0.20%
Japonica Intermediate	241	50.20%	2.90%	46.47%	0.00%	CTGTTTACGAAAAACACGA: 0.41%
VI/Aromatic	96	81.20%	0.00%	18.75%	0.00%	NA
Intermediate	90	70.00%	2.20%	26.67%	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
vg1120148591	C -> T	LOC_Os11g34370.1	upstream_gene_variant ; 655.0bp to feature; MODIFIER	silent_mutation	Average:79.508; most accessible tissue: Zhenshan97 flower, score: 88.021	N	N	N	N
vg1120148591	C -> T	LOC_Os11g34390.1	downstream_gene_variant ; 3905.0bp to feature; MODIFIER	silent_mutation	Average:79.508; most accessible tissue: Zhenshan97 flower, score: 88.021	N	N	N	N
vg1120148591	C -> T	LOC_Os11g34380.1	intron_variant ; MODIFIER	silent_mutation	Average:79.508; most accessible tissue: Zhenshan97 flower, score: 88.021	N	N	N	N
vg1120148591	C -> CTGTTTACGAAAAACACGA	LOC_Os11g34370.1	upstream_gene_variant ; 656.0bp to feature; MODIFIER	silent_mutation	Average:79.508; most accessible tissue: Zhenshan97 flower, score: 88.021	N	N	N	N
vg1120148591	C -> CTGTTTACGAAAAACACGA	LOC_Os11g34390.1	downstream_gene_variant ; 3904.0bp to feature; MODIFIER	silent_mutation	Average:79.508; most accessible tissue: Zhenshan97 flower, score: 88.021	N	N	N	N
vg1120148591	C -> CTGTTTACGAAAAACACGA	LOC_Os11g34380.1	intron_variant ; MODIFIER	silent_mutation	Average:79.508; most accessible tissue: Zhenshan97 flower, score: 88.021	N	N	N	N
vg1120148591	C -> DEL	N	N	silent_mutation	Average:79.508; most accessible tissue: Zhenshan97 flower, score: 88.021	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1120148591	NA	9.81E-07	mr1229_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
vg1120148591	NA	3.00E-06	mr1693_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1120148591	NA	7.84E-06	mr1693_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1120148591	NA	1.47E-09	mr1741_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251