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Detailed information for vg1128340436:

Variant ID: vg1128340436 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 28340436
Reference Allele: GAACTC	Alternative Allele: TAACTC,G
Primary Allele: TAACTC	Secondary Allele: GAACTC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTGCTACCGTGTTCGATTTCTGCGGAAGCTTGTGGATATTTTTGCTTCTGCTGGGGAATTTGAGCAGTGGTAGCCTGGATTGTAATTTACTAATTTGTG[GAACTC/TAACTC,G]
CATGCAAAAATGAAAGCTATTTTGGACAAATCACTTATGCATGTTTGATGTTTGTCTGTCTATTTTAAATTGCCACACGCAGCACCCAAAATCCAACTCA

Reverse complement sequence

TGAGTTGGATTTTGGGTGCTGCGTGTGGCAATTTAAAATAGACAGACAAACATCAAACATGCATAAGTGATTTGTCCAAAATAGCTTTCATTTTTGCATG[GAGTTC/GAGTTA,C]
CACAAATTAGTAAATTACAATCCAGGCTACCACTGCTCAAATTCCCCAGCAGAAGCAAAAATATCCACAAGCTTCCGCAGAAATCGAACACGGTAGCACT

Allele Frequencies:

Populations	Population Size	Frequency of TAACTC(primary allele)	Frequency of GAACTC(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	30.00%	11.00%	10.75%	47.95%	G: 0.36%
All Indica	2759	29.70%	7.90%	7.76%	54.15%	G: 0.43%
All Japonica	1512	27.00%	16.80%	17.59%	38.36%	G: 0.26%
Aus	269	28.60%	9.30%	7.06%	54.65%	G: 0.37%
Indica I	595	29.10%	14.50%	2.18%	54.29%	NA
Indica II	465	22.80%	1.90%	18.06%	56.34%	G: 0.86%
Indica III	913	35.00%	5.40%	3.94%	55.42%	G: 0.22%
Indica Intermediate	786	28.10%	9.50%	10.31%	51.27%	G: 0.76%
Temperate Japonica	767	21.00%	26.60%	21.90%	30.25%	G: 0.26%
Tropical Japonica	504	36.10%	4.20%	9.33%	50.40%	NA
Japonica Intermediate	241	27.00%	12.00%	21.16%	39.00%	G: 0.83%
VI/Aromatic	96	81.20%	6.20%	0.00%	12.50%	NA
Intermediate	90	36.70%	16.70%	10.00%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1128340436	GAACTC -> TAACTC	LOC_Os11g47120.1	upstream_gene_variant ; 1719.0bp to feature; MODIFIER	silent_mutation	Average:48.392; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg1128340436	GAACTC -> TAACTC	LOC_Os11g47130.1	intron_variant ; MODIFIER	silent_mutation	Average:48.392; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg1128340436	GAACTC -> DEL	N	N	silent_mutation	Average:48.392; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg1128340436	GAACTC -> G	LOC_Os11g47120.1	upstream_gene_variant ; 1720.0bp to feature; MODIFIER	silent_mutation	Average:48.392; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg1128340436	GAACTC -> G	LOC_Os11g47130.1	intron_variant ; MODIFIER	silent_mutation	Average:48.392; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1128340436	2.79E-06	2.79E-06	mr1464	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