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Detailed information for vg1112988477:

Variant ID: vg1112988477 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 12988477
Reference Allele: AGGTCTTTG	Alternative Allele: A,TGGTCTTTG
Primary Allele: AGGTCTTTG	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGACTTTTGGGCCGTGTATCGCGTTGGAACTCATTAGCGTTGCGTCGAGAGCGGGTTGCAAGACCCTAAACTCTATATATAAGTACCGCCGCCATCTTT[AGGTCTTTG/A,TGGTCTTTG]
GGTTTTGCTTAGATTAATCTGTCGAGAACAGTTTCGCCGCTAGATCGGTTTGTAAGACCACAACTCGTGAGCTTAATCATTCATCTGCAATTTTGGTTGT

Reverse complement sequence

ACAACCAAAATTGCAGATGAATGATTAAGCTCACGAGTTGTGGTCTTACAAACCGATCTAGCGGCGAAACTGTTCTCGACAGATTAATCTAAGCAAAACC[CAAAGACCT/T,CAAAGACCA]
AAAGATGGCGGCGGTACTTATATATAGAGTTTAGGGTCTTGCAACCCGCTCTCGACGCAACGCTAATGAGTTCCAACGCGATACACGGCCCAAAAGTCCA

Allele Frequencies:

Populations	Population Size	Frequency of AGGTCTTTG(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.30%	17.50%	18.37%	4.42%	TGGTCTTTG: 2.33%
All Indica	2759	35.30%	29.00%	28.31%	7.32%	TGGTCTTTG: 0.04%
All Japonica	1512	89.00%	0.60%	3.51%	0.00%	TGGTCTTTG: 6.94%
Aus	269	89.20%	3.30%	6.32%	1.12%	NA
Indica I	595	48.70%	15.50%	31.76%	4.03%	NA
Indica II	465	27.50%	32.70%	26.24%	13.55%	NA
Indica III	913	26.80%	38.10%	28.81%	6.24%	NA
Indica Intermediate	786	39.60%	26.60%	26.34%	7.38%	TGGTCTTTG: 0.13%
Temperate Japonica	767	83.10%	0.00%	3.39%	0.00%	TGGTCTTTG: 13.56%
Tropical Japonica	504	93.80%	1.60%	4.56%	0.00%	NA
Japonica Intermediate	241	97.50%	0.40%	1.66%	0.00%	TGGTCTTTG: 0.41%
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	62.20%	10.00%	18.89%	4.44%	TGGTCTTTG: 4.44%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1112988477	AGGTCTTTG -> DEL	N	N	silent_mutation	Average:9.904; most accessible tissue: Callus, score: 19.309	N	N	N	N
vg1112988477	AGGTCTTTG -> A	LOC_Os11g22570.1	upstream_gene_variant ; 4119.0bp to feature; MODIFIER	silent_mutation	Average:9.904; most accessible tissue: Callus, score: 19.309	N	N	N	N
vg1112988477	AGGTCTTTG -> A	LOC_Os11g22580.1	intron_variant ; MODIFIER	silent_mutation	Average:9.904; most accessible tissue: Callus, score: 19.309	N	N	N	N
vg1112988477	AGGTCTTTG -> TGGTCTTTG	LOC_Os11g22570.1	upstream_gene_variant ; 4118.0bp to feature; MODIFIER	silent_mutation	Average:9.904; most accessible tissue: Callus, score: 19.309	N	N	N	N
vg1112988477	AGGTCTTTG -> TGGTCTTTG	LOC_Os11g22580.1	intron_variant ; MODIFIER	silent_mutation	Average:9.904; most accessible tissue: Callus, score: 19.309	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1112988477	1.59E-06	2.50E-07	mr1338_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
vg1112988477	NA	2.81E-06	mr1576_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