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Detailed information for vg0608352038:

Variant ID: vg0608352038 (JBrowse)Variation Type: INDEL
Chromosome: chr06Position: 8352038
Reference Allele: TAAlternative Allele: AA,T
Primary Allele: TASecondary Allele: AA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTGAACATTTAGCTAGAGCAAATTGTTTCATGTAAATGAGACATGTCATTAACGAATAATTAATTAAGTAAACATGAAAAATTGATTTGCTTATTTTTT[TA/AA,T]
AAAAAGCTTATAAATATACTACCTCCGTTCCAAAATAAGTGCAGCCATATATATTCGTGTTTAGCATTTTGACCGTTCGTCTTATTTGAAAATTTTATGA

Reverse complement sequence

TCATAAAATTTTCAAATAAGACGAACGGTCAAAATGCTAAACACGAATATATATGGCTGCACTTATTTTGGAACGGAGGTAGTATATTTATAAGCTTTTT[TA/TT,A]
AAAAAATAAGCAAATCAATTTTTCATGTTTACTTAATTAATTATTCGTTAATGACATGTCTCATTTACATGAAACAATTTGCTCTAGCTAAATGTTCAAG

Allele Frequencies:

Populations Population SizeFrequency of TA(primary allele) Frequency of AA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.20% 21.50% 0.25% 0.00% T: 0.02%
All Indica  2759 98.20% 1.60% 0.14% 0.00% T: 0.04%
All Japonica  1512 44.70% 54.80% 0.46% 0.00% NA
Aus  269 92.60% 7.40% 0.00% 0.00% NA
Indica I  595 99.50% 0.00% 0.34% 0.00% T: 0.17%
Indica II  465 97.20% 2.60% 0.22% 0.00% NA
Indica III  913 98.40% 1.60% 0.00% 0.00% NA
Indica Intermediate  786 97.60% 2.30% 0.13% 0.00% NA
Temperate Japonica  767 72.90% 26.70% 0.39% 0.00% NA
Tropical Japonica  504 11.50% 88.10% 0.40% 0.00% NA
Japonica Intermediate  241 24.50% 74.70% 0.83% 0.00% NA
VI/Aromatic  96 6.20% 93.80% 0.00% 0.00% NA
Intermediate  90 63.30% 35.60% 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
vg0608352038 TA -> AA LOC_Os06g14750-LOC_Os06g14770 intergenic_region ; MODIFIER silent_mutation Average:38.507; most accessible tissue: Zhenshan97 root, score: 56.557 N N N N
vg0608352038 TA -> T LOC_Os06g14750-LOC_Os06g14770 intergenic_region ; MODIFIER silent_mutation Average:38.507; most accessible tissue: Zhenshan97 root, score: 56.557 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0608352038 NA 3.06E-10 mr1322 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
vg0608352038 NA 1.23E-13 mr1449 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
vg0608352038 NA 2.06E-06 mr1527 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
vg0608352038 NA 3.52E-08 mr1648 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
vg0608352038 3.65E-06 3.39E-20 mr1281_2 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
vg0608352038 NA 2.64E-09 mr1398_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
vg0608352038 NA 1.11E-07 mr1408_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
vg0608352038 NA 7.99E-17 mr1552_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
vg0608352038 NA 6.65E-08 mr1783_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
vg0608352038 NA 3.00E-07 mr1804_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
vg0608352038 5.64E-07 NA mr1829_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
vg0608352038 7.06E-06 NA mr1902_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