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Detailed information for vg1120967837:

Variant ID: vg1120967837 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 20967837
Reference Allele: C	Alternative Allele: T,CGT
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGAGTTAGGAACTCCAGCAAATGCCCTGTTTGGGAGAGCTTCTCCCAGCTGCAGCTTTTCTCAAAAGCTGCTTCTGCTAGAAGCTGCCCCAAACAGTCCA[C/T,CGT]
AGCTTCTGAGAATCTGTAGTTACAGATTCTGAAAAATAAACTAAGAAACCAGAAGCTGGAGAAACTGGGTTTCAGAGTTTTTCCAGATTTTTAAAAGCTG

Reverse complement sequence

CAGCTTTTAAAAATCTGGAAAAACTCTGAAACCCAGTTTCTCCAGCTTCTGGTTTCTTAGTTTATTTTTCAGAATCTGTAACTACAGATTCTCAGAAGCT[G/A,ACG]
TGGACTGTTTGGGGCAGCTTCTAGCAGAAGCAGCTTTTGAGAAAAGCTGCAGCTGGGAGAAGCTCTCCCAAACAGGGCATTTGCTGGAGTTCCTAACTCC

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	93.10%	5.50%	0.19%	1.14%	CGT: 0.02%
All Indica	2759	94.50%	4.30%	0.07%	1.09%	NA
All Japonica	1512	98.30%	0.30%	0.07%	1.39%	NA
Aus	269	47.60%	49.40%	2.23%	0.37%	CGT: 0.37%
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	84.50%	12.90%	0.00%	2.58%	NA
Indica III	913	97.90%	1.20%	0.00%	0.88%	NA
Indica Intermediate	786	92.40%	6.10%	0.25%	1.27%	NA
Temperate Japonica	767	99.60%	0.30%	0.00%	0.13%	NA
Tropical Japonica	504	96.00%	0.00%	0.00%	3.97%	NA
Japonica Intermediate	241	98.80%	0.80%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	6.70%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1120967837	C -> CGT	LOC_Os11g35720-LOC_Os11g35730	intergenic_region ; MODIFIER	silent_mutation	Average:62.609; most accessible tissue: Minghui63 panicle, score: 84.005	N	N	N	N
vg1120967837	C -> T	LOC_Os11g35720-LOC_Os11g35730	intergenic_region ; MODIFIER	silent_mutation	Average:62.609; most accessible tissue: Minghui63 panicle, score: 84.005	N	N	N	N
vg1120967837	C -> DEL	N	N	silent_mutation	Average:62.609; most accessible tissue: Minghui63 panicle, score: 84.005	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1120967837	2.85E-06	1.19E-07	mr1612_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