Search for Variation information by Variation ID:

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

Detailed information for vg0624062700:

Variant ID: vg0624062700 (JBrowse)	Variation Type: INDEL
Chromosome: chr06	Position: 24062700
Reference Allele: TGTA	Alternative Allele: CGTA,T
Primary Allele: TGTA	Secondary Allele: CGTA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTCGCTCTCTATAGGCTGGCTACCAGGCCCCTTTCCAAACACTACTTTAAGATCTTTAACCATAGCAAACACTGTTTTCCCGCTGCGATGTTTAGGCTT[TGTA/CGTA,T]
CAGTGGTCCTCCTTATGTTCAAAGTGCTTGCCTTTCTTCCGTACCGGGTGGTTTGCTGCAAGGAATCGACGATAACCCATGTACACAACCTTCCTACAGT

Reverse complement sequence

ACTGTAGGAAGGTTGTGTACATGGGTTATCGTCGATTCCTTGCAGCAAACCACCCGGTACGGAAGAAAGGCAAGCACTTTGAACATAAGGAGGACCACTG[TACA/TACG,A]
AAGCCTAAACATCGCAGCGGGAAAACAGTGTTTGCTATGGTTAAAGATCTTAAAGTAGTGTTTGGAAAGGGGCCTGGTAGCCAGCCTATAGAGAGCGAAG

Allele Frequencies:

Populations	Population Size	Frequency of TGTA(primary allele)	Frequency of CGTA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.40%	0.20%	19.85%	37.60%	NA
All Indica	2759	16.20%	0.30%	21.35%	62.16%	NA
All Japonica	1512	89.20%	0.10%	8.80%	1.92%	NA
Aus	269	26.40%	0.00%	71.00%	2.60%	NA
Indica I	595	4.50%	0.20%	6.05%	89.24%	NA
Indica II	465	11.80%	0.20%	19.78%	68.17%	NA
Indica III	913	28.30%	0.00%	29.90%	41.84%	NA
Indica Intermediate	786	13.60%	0.80%	23.92%	61.70%	NA
Temperate Japonica	767	96.70%	0.00%	1.56%	1.69%	NA
Tropical Japonica	504	74.60%	0.20%	22.42%	2.78%	NA
Japonica Intermediate	241	95.90%	0.00%	3.32%	0.83%	NA
VI/Aromatic	96	83.30%	0.00%	16.67%	0.00%	NA
Intermediate	90	61.10%	0.00%	10.00%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0624062700	TGTA -> CGTA	LOC_Os06g40410.1	synonymous_variant ; p.Thr532Thr; LOW	synonymous_codon	Average:21.175; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0624062700	TGTA -> T	LOC_Os06g40410.1	stop_gained&disruptive_inframe_deletion ; p.Cys531_Thr532delinsTer; HIGH	N	Average:21.175; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0624062700	TGTA -> DEL	LOC_Os06g40410.1	N	frameshift_variant	Average:21.175; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0624062700	NA	8.45E-09	mr1111	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
vg0624062700	NA	1.97E-07	mr1144	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
vg0624062700	NA	1.22E-07	mr1213	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
vg0624062700	NA	7.26E-06	mr1215	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
vg0624062700	NA	1.91E-08	mr1234	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
vg0624062700	NA	2.85E-08	mr1442	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
vg0624062700	NA	1.32E-07	mr1111_2	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
vg0624062700	NA	1.57E-08	mr1144_2	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
vg0624062700	NA	2.24E-06	mr1380_2	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
vg0624062700	NA	8.48E-07	mr1548_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
vg0624062700	NA	3.85E-07	mr1561_2	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
vg0624062700	NA	5.95E-07	mr1676_2	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
vg0624062700	3.01E-08	6.55E-12	mr1807_2	Ind_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
vg0624062700	NA	8.15E-06	mr1908_2	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