\

Search for Variation information by Variation ID:

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

Detailed information for vg0510158281:

Variant ID: vg0510158281 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 10158281
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGAGCGACATCGACGAGTCCTTTCGTTTTAGCCACCTTTTTGATAGGACCTCCCTTCGCCGCCGCGCCCGAAGAGAACGCAACTAGGGCCTTCGCCCCTT[C/T]
CAAATCCTTCCGACGAAGGGGGGAGCTGTTCGACTCCACCCCGGTTTCGTTGTTACCAGGACTTGGGGTAGGAGTGTACCCTGGGGTGTCGGCGCGGTTT

Reverse complement sequence

AAACCGCGCCGACACCCCAGGGTACACTCCTACCCCAAGTCCTGGTAACAACGAAACCGGGGTGGAGTCGAACAGCTCCCCCCTTCGTCGGAAGGATTTG[G/A]
AAGGGGCGAAGGCCCTAGTTGCGTTCTCTTCGGGCGCGGCGGCGAAGGGAGGTCCTATCAAAAAGGTGGCTAAAACGAAAGGACTCGTCGATGTCGCTCG

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 98.90% 0.70% 0.42% 0.00% NA
All Indica  2759 98.10% 1.20% 0.72% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.50% 1.00% 1.51% 0.00% NA
Indica II  465 97.00% 1.70% 1.29% 0.00% NA
Indica III  913 99.30% 0.40% 0.22% 0.00% NA
Indica Intermediate  786 97.80% 1.80% 0.38% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0510158281 C -> T LOC_Os05g17640.1 downstream_gene_variant ; 1661.0bp to feature; MODIFIER silent_mutation Average:59.956; most accessible tissue: Zhenshan97 flag leaf, score: 82.874 N N N N
vg0510158281 C -> T LOC_Os05g17650.1 intron_variant ; MODIFIER silent_mutation Average:59.956; most accessible tissue: Zhenshan97 flag leaf, score: 82.874 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0510158281 NA 8.75E-06 mr1128 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
vg0510158281 NA 2.99E-06 mr1229 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
vg0510158281 5.05E-06 5.05E-06 mr1393 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
vg0510158281 8.06E-06 8.06E-06 mr1605 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