\

Search for Variation information by Variation ID:

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

Detailed information for vg0613825382:

Variant ID: vg0613825382 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 13825382
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


TAGTATTGATGTTGGTTTAGTGCCACCGCTCCGGTGTTGGTTAACTAAAATATGCTAAATGATTGGCTGTGGGTGTATGGTTTTGATGGTCGCGCCCATG[G/A]
CAGTTAAGTACCGGTTCGCGGGATGCCCTAGAAGAACTTATCGTACTTACCACAAGCCAGCTTGGGCAACGGTTGGGCTTGTAGTGTAGCTTTCCTCTAG

Reverse complement sequence

CTAGAGGAAAGCTACACTACAAGCCCAACCGTTGCCCAAGCTGGCTTGTGGTAAGTACGATAAGTTCTTCTAGGGCATCCCGCGAACCGGTACTTAACTG[C/T]
CATGGGCGCGACCATCAAAACCATACACCCACAGCCAATCATTTAGCATATTTTAGTTAACCAACACCGGAGCGGTGGCACTAAACCAACATCAATACTA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.80% 10.20% 0.08% 0.00% NA
All Indica  2759 83.50% 16.40% 0.11% 0.00% NA
All Japonica  1512 98.80% 1.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 87.10% 12.90% 0.00% 0.00% NA
Indica III  913 71.70% 28.30% 0.00% 0.00% NA
Indica Intermediate  786 83.60% 16.00% 0.38% 0.00% NA
Temperate Japonica  767 98.60% 1.40% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 10.00% 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
vg0613825382 G -> A LOC_Os06g23670-LOC_Os06g23684 intergenic_region ; MODIFIER silent_mutation Average:53.012; most accessible tissue: Zhenshan97 young leaf, score: 71.497 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0613825382 5.33E-06 NA mr1068 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
vg0613825382 4.81E-07 NA mr1110 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
vg0613825382 5.20E-06 NA mr1121 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
vg0613825382 3.61E-06 NA mr1144 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
vg0613825382 8.56E-06 NA mr1121_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