Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1119925776:

Variant ID: vg1119925776 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 19925776
Reference Allele: GT	Alternative Allele: AT,GTT,TT,GTTT,G
Primary Allele: GT	Secondary Allele: AT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTAATGTACTTAGGCTGCGTTTTTTTTTTCTTTTCCTTTCACAACATCTACAGTACTGTCGTTTTTCATCCACGCGTTTCCTAAATTACTAAACAGTTT[GT/AT,GTT,TT,GTTT,G]
TTTTTAAAAAAAAATATAGCAAAGTTAATTTTAAGAATAATATTATTCTATTTTTAAAGTGAATTTTACTGATACTTAATTAATCATGCACTAATAACTC

Reverse complement sequence

GAGTTATTAGTGCATGATTAATTAAGTATCAGTAAAATTCACTTTAAAAATAGAATAATATTATTCTTAAAATTAACTTTGCTATATTTTTTTTTAAAAA[AC/AT,AAC,AA,AAAC,C]
AAACTGTTTAGTAATTTAGGAAACGCGTGGATGAAAAACGACAGTACTGTAGATGTTGTGAAAGGAAAAGAAAAAAAAAACGCAGCCTAAGTACATTAAA

Allele Frequencies:

Populations	Population Size	Frequency of GT(primary allele)	Frequency of AT(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.20%	42.60%	0.34%	0.00%	TT: 3.51%; GTTT: 0.74%; GTT: 0.55%; G: 0.11%
All Indica	2759	32.30%	66.40%	0.36%	0.00%	TT: 0.65%; G: 0.18%; GTTT: 0.11%
All Japonica	1512	93.20%	6.40%	0.13%	0.00%	GTT: 0.26%
Aus	269	16.40%	16.40%	1.12%	0.00%	TT: 53.90%; GTTT: 11.90%; GTT: 0.37%
Indica I	595	41.80%	57.00%	0.50%	0.00%	TT: 0.50%; G: 0.17%
Indica II	465	35.30%	63.90%	0.00%	0.00%	TT: 0.86%
Indica III	913	22.20%	76.70%	0.22%	0.00%	G: 0.44%; GTTT: 0.33%; TT: 0.11%
Indica Intermediate	786	34.90%	63.20%	0.64%	0.00%	TT: 1.27%
Temperate Japonica	767	94.10%	5.70%	0.13%	0.00%	NA
Tropical Japonica	504	90.50%	9.30%	0.20%	0.00%	NA
Japonica Intermediate	241	95.90%	2.50%	0.00%	0.00%	GTT: 1.66%
VI/Aromatic	96	77.10%	3.10%	1.04%	0.00%	GTT: 18.75%
Intermediate	90	53.30%	40.00%	0.00%	0.00%	TT: 3.33%; GTT: 3.33%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1119925776	GT -> GTT	LOC_Os11g34070.1	intron_variant ; MODIFIER	silent_mutation	Average:52.674; most accessible tissue: Zhenshan97 flower, score: 74.708	N	N	N	N
vg1119925776	GT -> AT	LOC_Os11g34070.1	intron_variant ; MODIFIER	silent_mutation	Average:52.674; most accessible tissue: Zhenshan97 flower, score: 74.708	N	N	N	N
vg1119925776	GT -> TT	LOC_Os11g34070.1	intron_variant ; MODIFIER	silent_mutation	Average:52.674; most accessible tissue: Zhenshan97 flower, score: 74.708	N	N	N	N
vg1119925776	GT -> GTTT	LOC_Os11g34070.1	intron_variant ; MODIFIER	silent_mutation	Average:52.674; most accessible tissue: Zhenshan97 flower, score: 74.708	N	N	N	N
vg1119925776	GT -> G	LOC_Os11g34070.1	intron_variant ; MODIFIER	silent_mutation	Average:52.674; most accessible tissue: Zhenshan97 flower, score: 74.708	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119925776	NA	1.42E-09	mr1047	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
vg1119925776	NA	4.22E-06	mr1189	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
vg1119925776	4.12E-06	NA	mr1684	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
vg1119925776	NA	2.03E-22	mr1888	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
vg1119925776	NA	2.95E-06	mr1990	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
vg1119925776	NA	9.83E-28	mr1323_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