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Detailed information for vg0510317154:

Variant ID: vg0510317154 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 10317154
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.63, C: 0.36, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


CATTATAACAGACAATGGCTCCCAGTTCATCAGTGCCGACTTCCAGGATTACTGCATTGGATTGGGAGTCAAGATTTGCTTTGCCTCGGTTTCTCACCCT[T/C]
AGAGCAATGGACAGGTCAAAAGGGCAAATGGCATAGTACTACAAGGGATCAAGACCCGTGTCTACGATAGACTCATGTCACATGACAAGAAGTGGGTCGA

Reverse complement sequence

TCGACCCACTTCTTGTCATGTGACATGAGTCTATCGTAGACACGGGTCTTGATCCCTTGTAGTACTATGCCATTTGCCCTTTTGACCTGTCCATTGCTCT[A/G]
AGGGTGAGAAACCGAGGCAAAGCAAATCTTGACTCCCAATCCAATGCAGTAATCCTGGAAGTCGGCACTGATGAACTGGGAGCCATTGTCTGTTATAATG

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 96.90% 3.10% 0.02% 0.00% NA
All Indica  2759 94.90% 5.10% 0.04% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 91.80% 8.10% 0.17% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 94.40% 5.60% 0.00% 0.00% NA
Indica Intermediate  786 95.00% 5.00% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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 97.80% 2.20% 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
vg0510317154 T -> C LOC_Os05g17950.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:51.259; most accessible tissue: Minghui63 flag leaf, score: 74.161 N N N N
vg0510317154 T -> C LOC_Os05g17960.1 upstream_gene_variant ; 3998.0bp to feature; MODIFIER silent_mutation Average:51.259; most accessible tissue: Minghui63 flag leaf, score: 74.161 N N N N
vg0510317154 T -> C LOC_Os05g17940.1 downstream_gene_variant ; 1795.0bp to feature; MODIFIER silent_mutation Average:51.259; most accessible tissue: Minghui63 flag leaf, score: 74.161 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0510317154 4.74E-06 4.74E-06 mr1666 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