Search for Variation information by Variation ID:

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

Detailed information for vg0501904125:

Variant ID: vg0501904125 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 1904125
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATATCTCCGTTGATTCTTAAGGACGGTTTTATTTTTGATATTTTCATGCTTGAGGAGGCATTGAGAGATACATACTCCATCTATAATTTTTAAAAGTGT[C/A]
TTTTTAGTTATAAACCTGAACTCTCTTTTAGGGACGGAGCTAGCTAGGGGGTATTTTATTGTATTAAGTTTGGCACCTATGGGTAGATGTGATCGTAAAA

Reverse complement sequence

TTTTACGATCACATCTACCCATAGGTGCCAAACTTAATACAATAAAATACCCCCTAGCTAGCTCCGTCCCTAAAAGAGAGTTCAGGTTTATAACTAAAAA[G/T]
ACACTTTTAAAAATTATAGATGGAGTATGTATCTCTCAATGCCTCCTCAAGCATGAAAATATCAAAAATAAAACCGTCCTTAAGAATCAACGGAGATATT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.90% 16.10% 0.00% 0.02% NA
All Indica  2759 99.20% 0.80% 0.00% 0.00% NA
All Japonica  1512 57.40% 42.50% 0.00% 0.07% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 98.60% 1.40% 0.00% 0.00% NA
Temperate Japonica  767 75.20% 24.80% 0.00% 0.00% NA
Tropical Japonica  504 37.90% 61.90% 0.00% 0.20% NA
Japonica Intermediate  241 41.50% 58.50% 0.00% 0.00% NA
VI/Aromatic  96 17.70% 82.30% 0.00% 0.00% NA
Intermediate  90 80.00% 20.00% 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
vg0501904125 C -> DEL N N silent_mutation Average:44.889; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N
vg0501904125 C -> A LOC_Os05g04210.1 downstream_gene_variant ; 3790.0bp to feature; MODIFIER silent_mutation Average:44.889; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N
vg0501904125 C -> A LOC_Os05g04190-LOC_Os05g04210 intergenic_region ; MODIFIER silent_mutation Average:44.889; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0501904125 7.90E-06 6.91E-08 mr1269 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
vg0501904125 NA 7.48E-07 mr1278 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
vg0501904125 NA 5.67E-07 mr1723 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
vg0501904125 NA 2.53E-12 mr1775 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
vg0501904125 NA 7.85E-07 mr1797 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
vg0501904125 NA 7.85E-07 mr1801 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
vg0501904125 NA 9.43E-06 mr1768_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