Search for Variation information by Variation ID:

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

Detailed information for vg0402160287:

Variant ID: vg0402160287 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 2160287
Reference Allele: TAGTTTCTCG	Alternative Allele: AAGTTTCTCG,T
Primary Allele: TAGTTTCTCG	Secondary Allele: AAGTTTCTCG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCACTGCTACTCCACCGGCTGAGATTACGTGGCCTAGGAAAGCGACTTCTTTTAACCAGAACTCACATTTACTAAACTTTGCATATAATTTATGCTTCTG[TAGTTTCTCG/AAGTTTCTCG,T]
AGTACCAATCGCAAGTGTTCCGCATGTTCTTCCTCATCTTTGGAGTAGATTAGAATATCATCAATGAATACTACCACAAATTTGTCCAAGTAATCCATGA

Reverse complement sequence

TCATGGATTACTTGGACAAATTTGTGGTAGTATTCATTGATGATATTCTAATCTACTCCAAAGATGAGGAAGAACATGCGGAACACTTGCGATTGGTACT[CGAGAAACTA/CGAGAAACTT,A]
CAGAAGCATAAATTATATGCAAAGTTTAGTAAATGTGAGTTCTGGTTAAAAGAAGTCGCTTTCCTAGGCCACGTAATCTCAGCCGGTGGAGTAGCAGTGG

Allele Frequencies:

Populations	Population Size	Frequency of TAGTTTCTCG(primary allele)	Frequency of AAGTTTCTCG(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	34.30%	32.00%	1.84%	31.89%	T: 0.02%
All Indica	2759	24.80%	44.60%	1.99%	28.60%	NA
All Japonica	1512	48.20%	16.60%	0.86%	34.26%	T: 0.07%
Aus	269	58.00%	1.10%	1.86%	39.03%	NA
Indica I	595	42.20%	4.00%	2.02%	51.76%	NA
Indica II	465	43.70%	36.60%	1.94%	17.85%	NA
Indica III	913	3.60%	75.80%	1.75%	18.84%	NA
Indica Intermediate	786	25.20%	43.80%	2.29%	28.75%	NA
Temperate Japonica	767	75.00%	4.20%	1.04%	19.82%	NA
Tropical Japonica	504	14.70%	26.20%	0.60%	58.53%	NA
Japonica Intermediate	241	33.20%	36.10%	0.83%	29.46%	T: 0.41%
VI/Aromatic	96	10.40%	3.10%	7.29%	79.17%	NA
Intermediate	90	45.60%	25.60%	7.78%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402160287	TAGTTTCTCG -> DEL	LOC_Os04g04510.1	N	frameshift_variant	Average:9.178; most accessible tissue: Callus, score: 26.436	N	N	N	N
vg0402160287	TAGTTTCTCG -> AAGTTTCTCG	LOC_Os04g04510.1	synonymous_variant ; p.Leu300Leu; LOW	synonymous_codon	Average:9.178; most accessible tissue: Callus, score: 26.436	N	N	N	N
vg0402160287	TAGTTTCTCG -> T	LOC_Os04g04510.1	disruptive_inframe_deletion ; p.Glu298_Leu300del; MODERATE	inframe_variant	Average:9.178; most accessible tissue: Callus, score: 26.436	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402160287	7.58E-07	2.57E-08	mr1063_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
vg0402160287	NA	2.47E-07	mr1183_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