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Detailed information for vg1209095184:

Variant ID: vg1209095184 (JBrowse)	Variation Type: INDEL
Chromosome: chr12	Position: 9095184
Reference Allele: C	Alternative Allele: CTCTCTT,CTCTCTCTT,T,CTCTCTCTCTCTT,CTCTT,CTCTCTCTCTT
Primary Allele: C	Secondary Allele: CTCTCTT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTCATATAAGCAAATGTATATATTGTGTGACACAAATTTTTTTCAGTTTGAAACTTATTTTACTCAACCTCCATCCTCTCTCTCTCTCTCTCTCTCTCT[C/CTCTCTT,CTCTCTCTT,T,CTCTCTCTCTCTT,CTCTT,CTCTCTCTCTT]
TCACAAGAGAATTGTCATCAAATGTATTGATTCTTATGCATGCTATCTGAAAATTAATGTTATGTTCTCAGGTTCTGACCATTAACCAGTGGTACACATT

Reverse complement sequence

AATGTGTACCACTGGTTAATGGTCAGAACCTGAGAACATAACATTAATTTTCAGATAGCATGCATAAGAATCAATACATTTGATGACAATTCTCTTGTGA[G/AAGAGAG,AAGAGAGAG,A,AAGAGAGAGAGAG,AAGAG,AAGAGAGAGAG]
AGAGAGAGAGAGAGAGAGAGAGAGGATGGAGGTTGAGTAAAATAAGTTTCAAACTGAAAAAAATTTGTGTCACACAATATATACATTTGCTTATATGAGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of CTCTCTT(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	34.50%	22.00%	4.93%	23.85%	CTCTCTCTT: 6.12%; T: 4.66%; CTCTT: 2.33%; CTCTCTCTCTT: 1.02%; CTCTCTCTCTCTT: 0.68%
All Indica	2759	3.40%	36.10%	6.92%	38.35%	T: 6.27%; CTCTT: 3.62%; CTCTCTCTT: 3.59%; CTCTCTCTCTT: 1.09%; CTCTCTCTCTCTT: 0.62%
All Japonica	1512	94.20%	1.00%	0.60%	1.12%	T: 2.71%; CTCTT: 0.13%; CTCTCTCTCTCTT: 0.13%; CTCTCTCTT: 0.07%
Aus	269	3.00%	3.70%	10.04%	13.75%	CTCTCTCTT: 57.25%; CTCTCTCTCTT: 5.58%; CTCTCTCTCTCTT: 4.09%; CTCTT: 1.49%; T: 1.12%
Indica I	595	2.40%	15.50%	14.12%	53.11%	CTCTT: 6.22%; CTCTCTCTT: 4.54%; T: 4.03%; CTCTCTCTCTT: 0.17%
Indica II	465	5.20%	34.20%	3.87%	41.94%	T: 11.40%; CTCTCTCTT: 1.72%; CTCTT: 1.51%; CTCTCTCTCTCTT: 0.22%
Indica III	913	2.30%	52.00%	3.72%	26.40%	T: 5.37%; CTCTCTCTT: 4.38%; CTCTT: 3.07%; CTCTCTCTCTCTT: 1.53%; CTCTCTCTCTT: 1.20%
Indica Intermediate	786	4.50%	34.50%	7.00%	38.93%	T: 5.98%; CTCTT: 3.56%; CTCTCTCTT: 3.05%; CTCTCTCTCTT: 2.29%; CTCTCTCTCTCTT: 0.25%
Temperate Japonica	767	92.30%	0.40%	0.78%	1.43%	T: 4.95%; CTCTT: 0.13%
Tropical Japonica	504	95.60%	2.20%	0.40%	0.60%	T: 0.60%; CTCTCTCTCTCTT: 0.40%; CTCTT: 0.20%
Japonica Intermediate	241	97.50%	0.40%	0.41%	1.24%	CTCTCTCTT: 0.41%
VI/Aromatic	96	54.20%	6.20%	4.17%	4.17%	CTCTCTCTT: 28.12%; T: 1.04%; CTCTT: 1.04%; CTCTCTCTCTT: 1.04%
Intermediate	90	55.60%	11.10%	2.22%	12.22%	CTCTCTCTT: 8.89%; CTCTT: 3.33%; T: 2.22%; CTCTCTCTCTCTT: 2.22%; CTCTCTCTCTT: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1209095184	C -> CTCTCTCTCTT	LOC_Os12g15950.1	upstream_gene_variant ; 3723.0bp to feature; MODIFIER	silent_mutation	Average:56.352; most accessible tissue: Callus, score: 77.309	N	N	N	N
vg1209095184	C -> CTCTCTCTCTT	LOC_Os12g15960.1	upstream_gene_variant ; 2547.0bp to feature; MODIFIER	silent_mutation	Average:56.352; most accessible tissue: Callus, score: 77.309	N	N	N	N
vg1209095184	C -> CTCTCTCTCTT	LOC_Os12g15950-LOC_Os12g15960	intergenic_region ; MODIFIER	silent_mutation	Average:56.352; most accessible tissue: Callus, score: 77.309	N	N	N	N
vg1209095184	C -> CTCTCTCTCTCTT	LOC_Os12g15950.1	upstream_gene_variant ; 3723.0bp to feature; MODIFIER	silent_mutation	Average:56.352; most accessible tissue: Callus, score: 77.309	N	N	N	N
vg1209095184	C -> CTCTCTCTCTCTT	LOC_Os12g15960.1	upstream_gene_variant ; 2547.0bp to feature; MODIFIER	silent_mutation	Average:56.352; most accessible tissue: Callus, score: 77.309	N	N	N	N
vg1209095184	C -> CTCTCTCTCTCTT	LOC_Os12g15950-LOC_Os12g15960	intergenic_region ; MODIFIER	silent_mutation	Average:56.352; most accessible tissue: Callus, score: 77.309	N	N	N	N
vg1209095184	C -> CTCTT	LOC_Os12g15950.1	upstream_gene_variant ; 3723.0bp to feature; MODIFIER	silent_mutation	Average:56.352; most accessible tissue: Callus, score: 77.309	N	N	N	N
vg1209095184	C -> CTCTT	LOC_Os12g15960.1	upstream_gene_variant ; 2547.0bp to feature; MODIFIER	silent_mutation	Average:56.352; most accessible tissue: Callus, score: 77.309	N	N	N	N
vg1209095184	C -> CTCTT	LOC_Os12g15950-LOC_Os12g15960	intergenic_region ; MODIFIER	silent_mutation	Average:56.352; most accessible tissue: Callus, score: 77.309	N	N	N	N
vg1209095184	C -> CTCTCTCTT	LOC_Os12g15950.1	upstream_gene_variant ; 3723.0bp to feature; MODIFIER	silent_mutation	Average:56.352; most accessible tissue: Callus, score: 77.309	N	N	N	N
vg1209095184	C -> CTCTCTCTT	LOC_Os12g15960.1	upstream_gene_variant ; 2547.0bp to feature; MODIFIER	silent_mutation	Average:56.352; most accessible tissue: Callus, score: 77.309	N	N	N	N
vg1209095184	C -> CTCTCTCTT	LOC_Os12g15950-LOC_Os12g15960	intergenic_region ; MODIFIER	silent_mutation	Average:56.352; most accessible tissue: Callus, score: 77.309	N	N	N	N
vg1209095184	C -> T	LOC_Os12g15950.1	upstream_gene_variant ; 3722.0bp to feature; MODIFIER	silent_mutation	Average:56.352; most accessible tissue: Callus, score: 77.309	N	N	N	N
vg1209095184	C -> T	LOC_Os12g15960.1	upstream_gene_variant ; 2548.0bp to feature; MODIFIER	silent_mutation	Average:56.352; most accessible tissue: Callus, score: 77.309	N	N	N	N
vg1209095184	C -> T	LOC_Os12g15950-LOC_Os12g15960	intergenic_region ; MODIFIER	silent_mutation	Average:56.352; most accessible tissue: Callus, score: 77.309	N	N	N	N
vg1209095184	C -> DEL	N	N	silent_mutation	Average:56.352; most accessible tissue: Callus, score: 77.309	N	N	N	N
vg1209095184	C -> CTCTCTT	LOC_Os12g15950.1	upstream_gene_variant ; 3723.0bp to feature; MODIFIER	silent_mutation	Average:56.352; most accessible tissue: Callus, score: 77.309	N	N	N	N
vg1209095184	C -> CTCTCTT	LOC_Os12g15960.1	upstream_gene_variant ; 2547.0bp to feature; MODIFIER	silent_mutation	Average:56.352; most accessible tissue: Callus, score: 77.309	N	N	N	N
vg1209095184	C -> CTCTCTT	LOC_Os12g15950-LOC_Os12g15960	intergenic_region ; MODIFIER	silent_mutation	Average:56.352; most accessible tissue: Callus, score: 77.309	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1209095184	NA	1.77E-25	mr1350_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
vg1209095184	NA	2.03E-06	mr1350_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