Search for Variation information by Variation ID:

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

Detailed information for vg0405180721:

Variant ID: vg0405180721 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 5180721
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:


TTCAGGGACAAAATCACTCAAATTTCTAACTTTCCTAATCACTTCACGACTCATGCTCCATGACCTCCTTCTCCAGTTCCGGCGAACATGGAATGAACTC[T/C]
AACAAACTCAGACGAGCTCTAGAGCGGTTAGGTCTTCTGGTTGGCGATGGTAGGATGGGTGCAGGGTAGATGGGAGGAGTTCCCTGTGCAGTACGCCCCA

Reverse complement sequence

TGGGGCGTACTGCACAGGGAACTCCTCCCATCTACCCTGCACCCATCCTACCATCGCCAACCAGAAGACCTAACCGCTCTAGAGCTCGTCTGAGTTTGTT[A/G]
GAGTTCATTCCATGTTCGCCGGAACTGGAGAAGGAGGTCATGGAGCATGAGTCGTGAAGTGATTAGGAAAGTTAGAAATTTGAGTGATTTTGTCCCTGAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.90% 17.10% 0.00% 0.00% NA
All Indica  2759 96.80% 3.20% 0.00% 0.00% NA
All Japonica  1512 53.00% 47.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.80% 3.20% 0.00% 0.00% NA
Indica II  465 92.30% 7.70% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 96.40% 3.60% 0.00% 0.00% NA
Temperate Japonica  767 40.80% 59.20% 0.00% 0.00% NA
Tropical Japonica  504 80.60% 19.40% 0.00% 0.00% NA
Japonica Intermediate  241 34.40% 65.60% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0405180721 T -> C LOC_Os04g09654.1 intron_variant ; MODIFIER silent_mutation Average:58.938; most accessible tissue: Zhenshan97 young leaf, score: 78.938 N N N N
vg0405180721 T -> C LOC_Os04g09654.2 intron_variant ; MODIFIER silent_mutation Average:58.938; most accessible tissue: Zhenshan97 young leaf, score: 78.938 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0405180721 5.87E-06 NA mr1062 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
vg0405180721 NA 5.02E-07 mr1130 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
vg0405180721 NA 1.06E-07 mr1606 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
vg0405180721 NA 2.52E-09 mr1607 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
vg0405180721 NA 1.58E-08 mr1866 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
vg0405180721 1.68E-06 NA mr1631_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