Search for Variation information by Variation ID:

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

Detailed information for vg0524508210:

Variant ID: vg0524508210 (JBrowse)	Variation Type: INDEL
Chromosome: chr05	Position: 24508210
Reference Allele: GGAT	Alternative Allele: AGAT,G
Primary Allele: GGAT	Secondary Allele: AGAT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGCAGCTAAGGATTGCTTCGTCTACAAGCAGTTTGCAGAGCAATATGCCAAGAATGCACGGAAGACCCCTGACGGAGAACAAAGTACGTCGAAAAAGAA[GGAT/AGAT,G]
GATGATGATGATCCCCCGACAGGTTTTCAGGATCACCGTAAGGAGCTCAACCACATCTTTGGCGGCCCTCTGGCTTACGAGTCTAAAAGAAAGCAAAAGC

Reverse complement sequence

GCTTTTGCTTTCTTTTAGACTCGTAAGCCAGAGGGCCGCCAAAGATGTGGTTGAGCTCCTTACGGTGATCCTGAAAACCTGTCGGGGGATCATCATCATC[ATCC/ATCT,C]
TTCTTTTTCGACGTACTTTGTTCTCCGTCAGGGGTCTTCCGTGCATTCTTGGCATATTGCTCTGCAAACTGCTTGTAGACGAAGCAATCCTTAGCTGCGT

Allele Frequencies:

Populations	Population Size	Frequency of GGAT(primary allele)	Frequency of AGAT(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.10%	6.60%	0.25%	0.00%	G: 0.02%
All Indica	2759	100.00%	0.00%	0.04%	0.00%	NA
All Japonica	1512	78.90%	20.40%	0.66%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	94.50%	4.70%	0.78%	0.00%	NA
Tropical Japonica	504	50.80%	48.60%	0.60%	0.00%	NA
Japonica Intermediate	241	88.00%	11.60%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	0.00%	G: 1.04%
Intermediate	90	94.40%	4.40%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0524508210	GGAT -> G	LOC_Os05g41850.1	inframe_deletion ; p.Asp588del; MODERATE	inframe_variant	Average:31.294; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0524508210	GGAT -> AGAT	LOC_Os05g41850.1	synonymous_variant ; p.Lys583Lys; LOW	synonymous_codon	Average:31.294; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0524508210	NA	2.53E-07	mr1248	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
vg0524508210	NA	2.11E-07	mr1271	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
vg0524508210	NA	2.23E-06	mr1338	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
vg0524508210	NA	3.95E-07	mr1425	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
vg0524508210	NA	5.17E-06	mr1425	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
vg0524508210	NA	5.41E-09	mr1527	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
vg0524508210	NA	5.62E-11	mr1553	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
vg0524508210	NA	7.34E-06	mr1553	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
vg0524508210	NA	5.85E-08	mr1805	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
vg0524508210	NA	2.27E-08	mr1805_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