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Detailed information for vg0402455204:

Variant ID: vg0402455204 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 2455204
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCGTTGTATTAGGCTATATCTCATCTTTATCTATGTTTTTTTATGGACGGGAATATATCGTATAAAATGATTAACACTAAACTTAATATATTTGTAAAA[T/C]
GTTTTAGAAAAAGGATAAAGTGGAAGATCGGAAAAGGGACATTGGAACGCAGCTTTTAAGTCATTCGGATTTACTATGCGTTTGTTATAAGAAGAGGTTC

Reverse complement sequence

GAACCTCTTCTTATAACAAACGCATAGTAAATCCGAATGACTTAAAAGCTGCGTTCCAATGTCCCTTTTCCGATCTTCCACTTTATCCTTTTTCTAAAAC[A/G]
TTTTACAAATATATTAAGTTTAGTGTTAATCATTTTATACGATATATTCCCGTCCATAAAAAAACATAGATAAAGATGAGATATAGCCTAATACAACGAA

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 87.20% 12.00% 0.83% 0.00% NA
All Indica  2759 87.40% 12.50% 0.04% 0.00% NA
All Japonica  1512 85.00% 13.80% 1.26% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.20% 1.80% 0.00% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 75.10% 24.90% 0.00% 0.00% NA
Indica Intermediate  786 87.30% 12.60% 0.13% 0.00% NA
Temperate Japonica  767 97.70% 2.10% 0.26% 0.00% NA
Tropical Japonica  504 69.00% 27.80% 3.17% 0.00% NA
Japonica Intermediate  241 78.00% 21.60% 0.41% 0.00% NA
VI/Aromatic  96 77.10% 4.20% 18.75% 0.00% NA
Intermediate  90 90.00% 8.90% 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
vg0402455204 T -> C LOC_Os04g05040.1 upstream_gene_variant ; 4180.0bp to feature; MODIFIER silent_mutation Average:47.524; most accessible tissue: Callus, score: 94.211 N N N N
vg0402455204 T -> C LOC_Os04g05040-LOC_Os04g05050 intergenic_region ; MODIFIER silent_mutation Average:47.524; most accessible tissue: Callus, score: 94.211 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0402455204 NA 1.30E-09 Awn_length Ind_All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0402455204 NA 5.80E-07 mr1037 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
vg0402455204 4.66E-08 NA mr1798 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
vg0402455204 NA 1.27E-09 mr1798 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
vg0402455204 1.46E-19 NA mr1798_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
vg0402455204 8.62E-10 2.05E-14 mr1798_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
vg0402455204 4.25E-11 NA mr1798_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