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Detailed information for vg0311147041:

Variant ID: vg0311147041 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 11147041
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCCAGGTGAGGTTGGCCGAGGCCCAATAACTTAAGGTTGCCCGGACCCCAACAGTTCATAGGCACACCCACTCGGGGAAAGGCCCAATCTCCAGTTCATA[G/A]
GCACACCCACTCGGGGAAAGGCCCAATCTCCCTAAAAGACTAGTCCGGTAGGGGAAGGGTGGCTCTCCCTTTTAAGGTGGCTTCCTCCTCCCAAGCTAAG

Reverse complement sequence

CTTAGCTTGGGAGGAGGAAGCCACCTTAAAAGGGAGAGCCACCCTTCCCCTACCGGACTAGTCTTTTAGGGAGATTGGGCCTTTCCCCGAGTGGGTGTGC[C/T]
TATGAACTGGAGATTGGGCCTTTCCCCGAGTGGGTGTGCCTATGAACTGTTGGGGTCCGGGCAACCTTAAGTTATTGGGCCTCGGCCAACCTCACCTGGG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.40% 3.50% 1.10% 0.00% NA
All Indica  2759 92.10% 6.00% 1.85% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 93.90% 1.80% 4.20% 0.00% NA
Indica II  465 98.30% 1.50% 0.22% 0.00% NA
Indica III  913 86.40% 12.60% 0.99% 0.00% NA
Indica Intermediate  786 93.80% 4.20% 2.04% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 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
vg0311147041 G -> A LOC_Os03g19800.1 intron_variant ; MODIFIER silent_mutation Average:68.857; most accessible tissue: Minghui63 young leaf, score: 80.234 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0311147041 9.66E-06 9.66E-06 mr1524 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
vg0311147041 2.93E-06 1.43E-06 mr1671 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