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Detailed information for vg1127568993:

Variant ID: vg1127568993 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 27568993
Reference Allele: G	Alternative Allele: A,GA
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAACAGTTGCAGCCGGTAGCTCTTTACAACCACCATAGCTACAACAGTTGTGGCAGTAAGACCAATCGAACATACACATAGAAGGACAATGGCATGTACA[G/A,GA]
GCGAATCCAGCGTGGATGCTAGGGAGACTTACCGATTGAATCCCCCCTACCCCGCTAGATCTCTATTGATAGAAGGAGAGGGAAAGGGGGAGAAGAGGTA

Reverse complement sequence

TACCTCTTCTCCCCCTTTCCCTCTCCTTCTATCAATAGAGATCTAGCGGGGTAGGGGGGATTCAATCGGTAAGTCTCCCTAGCATCCACGCTGGATTCGC[C/T,TC]
TGTACATGCCATTGTCCTTCTATGTGTATGTTCGATTGGTCTTACTGCCACAACTGTTGTAGCTATGGTGGTTGTAAAGAGCTACCGGCTGCAACTGTTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	37.10%	6.50%	1.02%	55.33%	GA: 0.08%
All Indica	2759	39.10%	0.80%	0.80%	59.33%	GA: 0.04%
All Japonica	1512	35.10%	18.80%	1.72%	44.18%	GA: 0.20%
Aus	269	12.30%	0.00%	0.00%	87.73%	NA
Indica I	595	48.90%	0.30%	1.01%	49.75%	NA
Indica II	465	70.80%	0.90%	0.22%	28.17%	NA
Indica III	913	14.10%	0.70%	0.33%	84.78%	GA: 0.11%
Indica Intermediate	786	41.90%	1.10%	1.53%	55.47%	NA
Temperate Japonica	767	41.10%	31.90%	2.22%	24.77%	NA
Tropical Japonica	504	25.80%	2.20%	0.40%	71.23%	GA: 0.40%
Japonica Intermediate	241	35.70%	11.60%	2.90%	49.38%	GA: 0.41%
VI/Aromatic	96	67.70%	0.00%	0.00%	32.29%	NA
Intermediate	90	51.10%	1.10%	0.00%	47.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127568993	G -> GA	LOC_Os11g45530.1	upstream_gene_variant ; 1531.0bp to feature; MODIFIER	silent_mutation	Average:27.007; most accessible tissue: Callus, score: 84.612	N	N	N	N
vg1127568993	G -> GA	LOC_Os11g45540.1	downstream_gene_variant ; 2089.0bp to feature; MODIFIER	silent_mutation	Average:27.007; most accessible tissue: Callus, score: 84.612	N	N	N	N
vg1127568993	G -> GA	LOC_Os11g45530-LOC_Os11g45540	intergenic_region ; MODIFIER	silent_mutation	Average:27.007; most accessible tissue: Callus, score: 84.612	N	N	N	N
vg1127568993	G -> A	LOC_Os11g45530.1	upstream_gene_variant ; 1530.0bp to feature; MODIFIER	silent_mutation	Average:27.007; most accessible tissue: Callus, score: 84.612	N	N	N	N
vg1127568993	G -> A	LOC_Os11g45540.1	downstream_gene_variant ; 2090.0bp to feature; MODIFIER	silent_mutation	Average:27.007; most accessible tissue: Callus, score: 84.612	N	N	N	N
vg1127568993	G -> A	LOC_Os11g45530-LOC_Os11g45540	intergenic_region ; MODIFIER	silent_mutation	Average:27.007; most accessible tissue: Callus, score: 84.612	N	N	N	N
vg1127568993	G -> DEL	N	N	silent_mutation	Average:27.007; most accessible tissue: Callus, score: 84.612	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127568993	4.45E-07	4.45E-07	mr1972_2	Jap_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