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Detailed information for vg1106528916:

Variant ID: vg1106528916 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 6528916
Reference Allele: GCATATCTTCCATGGCTTCTGCGTGCCTTTTTGATAAAACTTATTATGTGA	Alternative Allele: ACATATCTTCCATGGCTTCTGCGTGCCTTTTTGATAAAACTTATTATGTGA,G
Primary Allele: GCATATCTTCCATGGCTTCT GCGTGCCTTTTTGATAAAAC TTATTATGTGA	Secondary Allele: ACATATCTTCCATGGCTTCT GCGTGCCTTTTTGATAAAAC TTATTATGTGA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGAAATAATGAACCGCTGATCATTGCTCTATTCAAGTAATTTTTATAAGCATCATTTACATAGTTGTGATGTGATTTTTTGGATAAATTTGGTTCTGTG[GCATATCTTCCATGGCTTCTGCGTGCCTTTTTGATAAAACTTATTATGTGA/ACATATCTTCCATGGCTTCTGCGTGCCTTTTTGATAAAACTTATTATGTGA,G]
CATATCTTCCATGGCTTATGTTCCCTGTTTTCCCAATCTAACCGAGCAGCAAAGCTTGAAGGATATGCAGCAAATAACCAATTTTTCTTCAACAACTATT

Reverse complement sequence

AATAGTTGTTGAAGAAAAATTGGTTATTTGCTGCATATCCTTCAAGCTTTGCTGCTCGGTTAGATTGGGAAAACAGGGAACATAAGCCATGGAAGATATG[TCACATAATAAGTTTTATCAAAAAGGCACGCAGAAGCCATGGAAGATATGC/TCACATAATAAGTTTTATCAAAAAGGCACGCAGAAGCCATGGAAGATATGT,C]
CACAGAACCAAATTTATCCAAAAAATCACATCACAACTATGTAAATGATGCTTATAAAAATTACTTGAATAGAGCAATGATCAGCGGTTCATTATTTCCT

Allele Frequencies:

Populations	Population Size	Frequency of GCATATCTTCCATGGCTTCT GCGTGCCTTTTTGATAAAAC TTATTATGTGA(primary allele)	Frequency of ACATATCTTCCATGGCTTCT GCGTGCCTTTTTGATAAAAC TTATTATGTGA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.60%	2.80%	2.26%	5.23%	G: 0.11%
All Indica	2759	88.50%	4.70%	3.33%	3.30%	G: 0.18%
All Japonica	1512	89.70%	0.00%	0.60%	9.72%	NA
Aus	269	99.30%	0.00%	0.37%	0.37%	NA
Indica I	595	84.40%	7.10%	5.88%	2.69%	NA
Indica II	465	94.00%	3.20%	1.51%	1.08%	G: 0.22%
Indica III	913	88.90%	3.30%	2.74%	4.60%	G: 0.44%
Indica Intermediate	786	87.80%	5.50%	3.18%	3.56%	NA
Temperate Japonica	767	85.50%	0.00%	0.78%	13.69%	NA
Tropical Japonica	504	96.80%	0.00%	0.40%	2.78%	NA
Japonica Intermediate	241	88.00%	0.00%	0.41%	11.62%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	86.70%	1.10%	3.33%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1106528916	GCATATCTTCCATGGCTTCTGCGTGCCTTTTTGATAAAACTTATTATGTGA -> ACATATCTTCCATGGCTTCTGCGTGCCTTT TTGATAAAACTTATTATGTGA	LOC_Os11g11750.1	upstream_gene_variant ; 2939.0bp to feature; MODIFIER	silent_mutation	Average:10.992; most accessible tissue: Zhenshan97 young leaf, score: 18.248	N	N	N	N
vg1106528916	GCATATCTTCCATGGCTTCTGCGTGCCTTTTTGATAAAACTTATTATGTGA -> ACATATCTTCCATGGCTTCTGCGTGCCTTT TTGATAAAACTTATTATGTGA	LOC_Os11g11760.1	upstream_gene_variant ; 2033.0bp to feature; MODIFIER	silent_mutation	Average:10.992; most accessible tissue: Zhenshan97 young leaf, score: 18.248	N	N	N	N
vg1106528916	GCATATCTTCCATGGCTTCTGCGTGCCTTTTTGATAAAACTTATTATGTGA -> ACATATCTTCCATGGCTTCTGCGTGCCTTT TTGATAAAACTTATTATGTGA	LOC_Os11g11770.1	downstream_gene_variant ; 3945.0bp to feature; MODIFIER	silent_mutation	Average:10.992; most accessible tissue: Zhenshan97 young leaf, score: 18.248	N	N	N	N
vg1106528916	GCATATCTTCCATGGCTTCTGCGTGCCTTTTTGATAAAACTTATTATGTGA -> ACATATCTTCCATGGCTTCTGCGTGCCTTT TTGATAAAACTTATTATGTGA	LOC_Os11g11750-LOC_Os11g11760	intergenic_region ; MODIFIER	silent_mutation	Average:10.992; most accessible tissue: Zhenshan97 young leaf, score: 18.248	N	N	N	N
vg1106528916	GCATATCTTCCATGGCTTCTGCGTGCCTTTTTGATAAAACTTATTATGTGA -> DEL	N	N	silent_mutation	Average:10.992; most accessible tissue: Zhenshan97 young leaf, score: 18.248	N	N	N	N
vg1106528916	GCATATCTTCCATGGCTTCTGCGTGCCTTTTTGATAAAACTTATTATGTGA -> G	LOC_Os11g11750.1	upstream_gene_variant ; 2940.0bp to feature; MODIFIER	silent_mutation	Average:10.992; most accessible tissue: Zhenshan97 young leaf, score: 18.248	N	N	N	N
vg1106528916	GCATATCTTCCATGGCTTCTGCGTGCCTTTTTGATAAAACTTATTATGTGA -> G	LOC_Os11g11760.1	upstream_gene_variant ; 2032.0bp to feature; MODIFIER	silent_mutation	Average:10.992; most accessible tissue: Zhenshan97 young leaf, score: 18.248	N	N	N	N
vg1106528916	GCATATCTTCCATGGCTTCTGCGTGCCTTTTTGATAAAACTTATTATGTGA -> G	LOC_Os11g11770.1	downstream_gene_variant ; 3944.0bp to feature; MODIFIER	silent_mutation	Average:10.992; most accessible tissue: Zhenshan97 young leaf, score: 18.248	N	N	N	N
vg1106528916	GCATATCTTCCATGGCTTCTGCGTGCCTTTTTGATAAAACTTATTATGTGA -> G	LOC_Os11g11750-LOC_Os11g11760	intergenic_region ; MODIFIER	silent_mutation	Average:10.992; most accessible tissue: Zhenshan97 young leaf, score: 18.248	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1106528916	NA	7.80E-06	mr1007	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
vg1106528916	NA	2.37E-06	mr1007	Ind_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
vg1106528916	4.57E-06	4.57E-06	mr1323	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
vg1106528916	NA	1.16E-06	mr1336	Ind_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
vg1106528916	NA	2.24E-06	mr1630	Ind_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
vg1106528916	NA	9.17E-06	mr1705	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