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Detailed information for vg0402468342:

Variant ID: vg0402468342 (JBrowse)Variation Type: INDEL
Chromosome: chr04Position: 2468342
Reference Allele: ACTAlternative Allele: A,GCT
Primary Allele: ACTSecondary Allele: GCT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATCCTTCACACCAATTAGACAAATAATATTAACCTTGGTTGTCGAAGAAAGCTTCGAAACTACGACATATAAGGCTGCATTCTTCAGTTTAAATTCCTC[ACT/A,GCT]
CTCTCGTTTAAACGCACGCATGCTTCCTAAATTGTTAAATGGTGTATGATTTGTAAAAATTTTCTGTAGAAAAGTTGCTTTAAAAATTATATTAATTTAT

Reverse complement sequence

ATAAATTAATATAATTTTTAAAGCAACTTTTCTACAGAAAATTTTTACAAATCATACACCATTTAACAATTTAGGAAGCATGCGTGCGTTTAAACGAGAG[AGT/T,AGC]
GAGGAATTTAAACTGAAGAATGCAGCCTTATATGTCGTAGTTTCGAAGCTTTCTTCGACAACCAAGGTTAATATTATTTGTCTAATTGGTGTGAAGGATA

Allele Frequencies:

Populations Population SizeFrequency of ACT(primary allele) Frequency of GCT(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.30% 12.00% 0.00% 1.21% A: 1.50%
All Indica  2759 96.10% 1.80% 0.00% 2.07% A: 0.04%
All Japonica  1512 80.60% 16.10% 0.00% 0.00% A: 3.24%
Aus  269 23.80% 76.20% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.00% 1.10% 0.00% 1.94% NA
Indica III  913 93.20% 3.10% 0.00% 3.72% NA
Indica Intermediate  786 96.10% 2.00% 0.00% 1.78% A: 0.13%
Temperate Japonica  767 97.10% 2.10% 0.00% 0.00% A: 0.78%
Tropical Japonica  504 64.10% 33.70% 0.00% 0.00% A: 2.18%
Japonica Intermediate  241 62.70% 24.10% 0.00% 0.00% A: 13.28%
VI/Aromatic  96 17.70% 60.40% 0.00% 0.00% A: 21.88%
Intermediate  90 88.90% 11.10% 0.00% 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
vg0402468342 ACT -> A LOC_Os04g05040-LOC_Os04g05050 intergenic_region ; MODIFIER silent_mutation Average:33.164; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N
vg0402468342 ACT -> DEL N N silent_mutation Average:33.164; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N
vg0402468342 ACT -> GCT LOC_Os04g05040-LOC_Os04g05050 intergenic_region ; MODIFIER silent_mutation Average:33.164; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0402468342 NA 1.10E-06 mr1224_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
vg0402468342 NA 4.33E-09 mr1642_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
vg0402468342 5.42E-09 NA mr1798_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
vg0402468342 1.12E-10 NA mr1798_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