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Detailed information for vg0430897454:

Variant ID: vg0430897454 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 30897454
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.05, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


TATTACATGAATATATTGTGTACACAGCACTGGTCCCCAATTCCCACCTTCATGCTAGATATTTTTAAAGACTACATAAATAAATTCATGAGACTTCAAA[T/C]
TTCTTTCGTCAGACAGACACGTCACTAATTGTTACAGGTTCCAGCAGACAGCCATCACATATTATAGCTACATACAATACACTGAAACCAGCAATTTTAT

Reverse complement sequence

ATAAAATTGCTGGTTTCAGTGTATTGTATGTAGCTATAATATGTGATGGCTGTCTGCTGGAACCTGTAACAATTAGTGACGTGTCTGTCTGACGAAAGAA[A/G]
TTTGAAGTCTCATGAATTTATTTATGTAGTCTTTAAAAATATCTAGCATGAAGGTGGGAATTGGGGACCAGTGCTGTGTACACAATATATTCATGTAATA

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 82.30% 17.70% 0.00% 0.00% NA
All Indica  2759 76.60% 23.40% 0.00% 0.00% NA
All Japonica  1512 89.20% 10.80% 0.00% 0.00% NA
Aus  269 92.20% 7.80% 0.00% 0.00% NA
Indica I  595 88.40% 11.60% 0.00% 0.00% NA
Indica II  465 97.00% 3.00% 0.00% 0.00% NA
Indica III  913 55.20% 44.80% 0.00% 0.00% NA
Indica Intermediate  786 80.50% 19.50% 0.00% 0.00% NA
Temperate Japonica  767 96.10% 3.90% 0.00% 0.00% NA
Tropical Japonica  504 94.60% 5.40% 0.00% 0.00% NA
Japonica Intermediate  241 56.00% 44.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0430897454 T -> C LOC_Os04g52020.1 intron_variant ; MODIFIER silent_mutation Average:52.926; most accessible tissue: Callus, score: 73.206 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0430897454 NA 2.34E-06 mr1534 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
vg0430897454 8.96E-07 7.68E-11 mr1745 Jap_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
vg0430897454 NA 6.24E-08 mr1745_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