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Detailed information for vg0613449469:

Variant ID: vg0613449469 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 13449469
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


ACTCTCCTCGACACCCTCCTCAAGGAAGACGCACTCAACCAAGCTGATCACGTCGTCAACATCTTGAACCAGACCAAGACCATGATTGCCGCCTCGGTCC[C/T]
GGTTAACTCCGCCAGCGTCCGCACGCCGACTTGCAGCCGAGTTCCCCATCTTCGATCTCAAGATTATCACCAGCCAAGTCTCAGCATCGCCGGAGCGGGA

Reverse complement sequence

TCCCGCTCCGGCGATGCTGAGACTTGGCTGGTGATAATCTTGAGATCGAAGATGGGGAACTCGGCTGCAAGTCGGCGTGCGGACGCTGGCGGAGTTAACC[G/A]
GGACCGAGGCGGCAATCATGGTCTTGGTCTGGTTCAAGATGTTGACGACGTGATCAGCTTGGTTGAGTGCGTCTTCCTTGAGGAGGGTGTCGAGGAGAGT

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 94.80% 5.10% 0.04% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 92.50% 7.40% 0.07% 0.00% NA
Aus  269 57.20% 42.80% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 80.60% 19.20% 0.20% 0.00% NA
Japonica Intermediate  241 94.20% 5.80% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 92.20% 6.70% 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
vg0613449469 C -> T LOC_Os06g23070.1 missense_variant&splice_region_variant ; p.Pro326Leu; MODERATE nonsynonymous_codon ; P326L Average:53.195; most accessible tissue: Zhenshan97 flag leaf, score: 71.63 unknown unknown DELETERIOUS 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0613449469 1.96E-11 NA mr1033 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
vg0613449469 7.31E-13 4.27E-17 mr1033 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
vg0613449469 2.49E-07 3.58E-11 mr1176 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
vg0613449469 8.91E-07 NA mr1536 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
vg0613449469 2.18E-14 NA mr1033_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
vg0613449469 1.55E-16 1.09E-22 mr1033_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
vg0613449469 9.54E-08 2.99E-09 mr1536_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