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Detailed information for vg0231359843:

Variant ID: vg0231359843 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 31359843
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCCGACCGGACGAGACGCACTGTCTCATCCGTGTCGTTTGAGAAGCACTCACTTAGTCGTTTTTAGAAAAGAGTTCAAATAAAATCAATTGCAAAAACAA[T/C]
AGCCTTTCTTTGAAGCCTGCATTAAACACTTATTTCCCATAGCTTGCTGAGTACTCCCGTACTCACCCTTGCTCTATATAAATAATCCCCCCCAGTTGCT

Reverse complement sequence

AGCAACTGGGGGGGATTATTTATATAGAGCAAGGGTGAGTACGGGAGTACTCAGCAAGCTATGGGAAATAAGTGTTTAATGCAGGCTTCAAAGAAAGGCT[A/G]
TTGTTTTTGCAATTGATTTTATTTGAACTCTTTTCTAAAAACGACTAAGTGAGTGCTTCTCAAACGACACGGATGAGACAGTGCGTCTCGTCCGGTCGGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 49.70% 0.00% 24.33% 25.98% NA
All Indica  2759 23.70% 0.00% 34.94% 41.36% NA
All Japonica  1512 99.60% 0.00% 0.13% 0.26% NA
Aus  269 10.80% 0.00% 61.71% 27.51% NA
Indica I  595 6.60% 0.00% 25.71% 67.73% NA
Indica II  465 37.60% 0.20% 30.75% 31.40% NA
Indica III  913 24.00% 0.00% 42.28% 33.73% NA
Indica Intermediate  786 28.00% 0.00% 35.88% 36.13% NA
Temperate Japonica  767 99.50% 0.00% 0.13% 0.39% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.00% 0.41% 0.41% NA
VI/Aromatic  96 96.90% 0.00% 3.12% 0.00% NA
Intermediate  90 73.30% 0.00% 16.67% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0231359843 T -> DEL N N silent_mutation Average:8.383; most accessible tissue: Zhenshan97 root, score: 20.427 N N N N
vg0231359843 T -> C LOC_Os02g51230-LOC_Os02g51240 intergenic_region ; MODIFIER silent_mutation Average:8.383; most accessible tissue: Zhenshan97 root, score: 20.427 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0231359843 4.27E-07 1.19E-07 mr1011 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