Search for Variation information by Variation ID:

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

Detailed information for vg0335310014:

Variant ID: vg0335310014 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 35310014
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.61, T: 0.39, others allele: 0.00, population size: 66. )

Flanking Sequence (100 bp) in Reference Genome:


GAAGGAAATGATGCCTCAGTGCTCAGTGCTTACTTTAGTACTCTCTATTCTATGAATTTAGACACGTAAAGCACATATATACATCAAAACAGCCGAAATT[C/T]
TGACAAATCGACCTTTAATAAAATTTATTTTGAAAATAGACCCAAAATATTCCTTACTTCCCTAAATGTTTGACGCTGTTGACTTTTTAAAGTATGTTTA

Reverse complement sequence

TAAACATACTTTAAAAAGTCAACAGCGTCAAACATTTAGGGAAGTAAGGAATATTTTGGGTCTATTTTCAAAATAAATTTTATTAAAGGTCGATTTGTCA[G/A]
AATTTCGGCTGTTTTGATGTATATATGTGCTTTACGTGTCTAAATTCATAGAATAGAGAGTACTAAAGTAAGCACTGAGCACTGAGGCATCATTTCCTTC

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 59.40% 40.50% 0.15% 0.00% NA
All Indica  2759 61.80% 38.10% 0.14% 0.00% NA
All Japonica  1512 54.70% 45.20% 0.07% 0.00% NA
Aus  269 80.70% 19.30% 0.00% 0.00% NA
Indica I  595 32.10% 67.40% 0.50% 0.00% NA
Indica II  465 79.40% 20.40% 0.22% 0.00% NA
Indica III  913 66.00% 34.00% 0.00% 0.00% NA
Indica Intermediate  786 69.00% 31.00% 0.00% 0.00% NA
Temperate Japonica  767 89.70% 10.20% 0.13% 0.00% NA
Tropical Japonica  504 11.10% 88.90% 0.00% 0.00% NA
Japonica Intermediate  241 34.40% 65.60% 0.00% 0.00% NA
VI/Aromatic  96 5.20% 93.80% 1.04% 0.00% NA
Intermediate  90 58.90% 40.00% 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
vg0335310014 C -> T LOC_Os03g62330.1 3_prime_UTR_variant ; 295.0bp to feature; MODIFIER silent_mutation Average:65.157; most accessible tissue: Minghui63 root, score: 80.163 N N N N
vg0335310014 C -> T LOC_Os03g62314.1 upstream_gene_variant ; 628.0bp to feature; MODIFIER silent_mutation Average:65.157; most accessible tissue: Minghui63 root, score: 80.163 N N N N
vg0335310014 C -> T LOC_Os03g62340.1 downstream_gene_variant ; 2437.0bp to feature; MODIFIER silent_mutation Average:65.157; most accessible tissue: Minghui63 root, score: 80.163 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0335310014 NA 5.26E-06 mr1606 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
vg0335310014 NA 1.20E-06 mr1183_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
vg0335310014 NA 2.54E-07 mr1338_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
vg0335310014 NA 6.46E-06 mr1383_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
vg0335310014 NA 1.23E-07 mr1794_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
vg0335310014 NA 1.19E-08 mr1910_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