Search for Variation information by Variation ID:

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

Detailed information for vg0500821426:

Variant ID: vg0500821426 (JBrowse)	Variation Type: INDEL
Chromosome: chr05	Position: 821426
Reference Allele: C	Alternative Allele: T,CTTAAAAGT
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

CCGAAGGGGGGTTCCCAACCGGCACCGTTTAGAGATTCTGTAGTAGTGAGTCTACGCTTAATATTTATAATTAGTGTCCAAACATCTGATGTGATAGGGA[C/T,CTTAAAAGT]
TTAAAAGTTTTAGTCCCGTCTAAACAGTGACAAAGGATCTTGAAAAGTTCAAATCTAGCTTATCACATTACATAACGCCTTCTCTAAACGGTTACAATTC

Reverse complement sequence

GAATTGTAACCGTTTAGAGAAGGCGTTATGTAATGTGATAAGCTAGATTTGAACTTTTCAAGATCCTTTGTCACTGTTTAGACGGGACTAAAACTTTTAA[G/A,ACTTTTAAG]
TCCCTATCACATCAGATGTTTGGACACTAATTATAAATATTAAGCGTAGACTCACTACTACAGAATCTCTAAACGGTGCCGGTTGGGAACCCCCCTTCGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.70%	36.70%	0.19%	0.00%	CTTAAAAGT: 0.36%
All Indica	2759	45.40%	54.30%	0.29%	0.00%	CTTAAAAGT: 0.04%
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	28.30%	71.70%	0.00%	0.00%	NA
Indica I	595	31.40%	68.40%	0.17%	0.00%	NA
Indica II	465	34.60%	65.20%	0.22%	0.00%	NA
Indica III	913	66.20%	33.60%	0.11%	0.00%	CTTAAAAGT: 0.11%
Indica Intermediate	786	38.20%	61.20%	0.64%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	97.10%	2.90%	0.00%	0.00%	NA
VI/Aromatic	96	71.90%	12.50%	0.00%	0.00%	CTTAAAAGT: 15.62%
Intermediate	90	73.30%	24.40%	1.11%	0.00%	CTTAAAAGT: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0500821426	C -> T	LOC_Os05g02435.1	upstream_gene_variant ; 119.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500821426	C -> T	LOC_Os05g02430-LOC_Os05g02435	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500821426	C -> CTTAAAAGT	LOC_Os05g02435.1	upstream_gene_variant ; 118.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500821426	C -> CTTAAAAGT	LOC_Os05g02430-LOC_Os05g02435	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0500821426	NA	2.69E-07	mr1190	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
vg0500821426	NA	7.04E-07	mr1418	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
vg0500821426	NA	2.73E-08	mr1420	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
vg0500821426	NA	7.07E-06	mr1445	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
vg0500821426	NA	8.49E-06	mr1508	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
vg0500821426	NA	3.74E-07	mr1739	Ind_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
vg0500821426	NA	3.88E-06	mr1812	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
vg0500821426	1.10E-06	1.10E-06	mr1954	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
vg0500821426	NA	7.32E-14	mr1216_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