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Detailed information for vg0513464420:

Variant ID: vg0513464420 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 13464420
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATCAAGTCATTTGGTTGATTACAATTATCAAAACCACTCGGTTGGTTGGATTATTTATTCCTTGACTATACGCTTAGTTTGTTCAGCTAACCACATAGT[C/T]
GGAGGCTACACCTATTAGGTGCATCTAGTCGATGCACCTAACTTTATTTTCCAACCCTCCACAGTCTAGTCGAAGATTATCTTTTCGACTATGAAGGTCT

Reverse complement sequence

AGACCTTCATAGTCGAAAAGATAATCTTCGACTAGACTGTGGAGGGTTGGAAAATAAAGTTAGGTGCATCGACTAGATGCACCTAATAGGTGTAGCCTCC[G/A]
ACTATGTGGTTAGCTGAACAAACTAAGCGTATAGTCAAGGAATAAATAATCCAACCAACCGAGTGGTTTTGATAATTGTAATCAACCAAATGACTTGATA

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 96.80% 2.30% 0.89% 0.00% NA
All Indica  2759 95.00% 3.80% 1.23% 0.00% NA
All Japonica  1512 99.50% 0.10% 0.46% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 98.20% 0.00% 1.85% 0.00% NA
Indica II  465 77.60% 19.80% 2.58% 0.00% NA
Indica III  913 99.80% 0.10% 0.11% 0.00% NA
Indica Intermediate  786 97.20% 1.50% 1.27% 0.00% NA
Temperate Japonica  767 99.20% 0.10% 0.65% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0513464420 C -> T LOC_Os05g23500-LOC_Os05g23520 intergenic_region ; MODIFIER silent_mutation Average:52.019; most accessible tissue: Minghui63 young leaf, score: 72.408 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0513464420 1.51E-12 5.67E-39 mr1039 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
vg0513464420 4.68E-09 2.63E-23 mr1039 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
vg0513464420 5.54E-11 NA mr1632 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
vg0513464420 3.01E-09 9.08E-13 mr1632 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
vg0513464420 3.08E-11 6.56E-44 mr1039_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
vg0513464420 1.35E-06 1.25E-25 mr1039_2 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
vg0513464420 NA 2.79E-08 mr1593_2 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
vg0513464420 2.02E-18 2.57E-33 mr1632_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
vg0513464420 4.99E-14 1.71E-21 mr1632_2 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