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Detailed information for vg0135925002:

Variant ID: vg0135925002 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35925002
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, G: 0.09, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


CAGCTGCTATCAAGGATTCTGGACTTTAGTCACAGTTGACAATATTTCAAAGTTGAGCACATCTTGAGATTTAGACTACTGTCCACAATTTCAAAGTTGT[C/G]
GCAAACCTTTCCAAGCCAAGTGTCAGACTCAAAAGCTCAGTTAATTACCAAACTTTTATCCAACACCCGAGACTTGTTTTAAGAAATATGACCAGTCACA

Reverse complement sequence

TGTGACTGGTCATATTTCTTAAAACAAGTCTCGGGTGTTGGATAAAAGTTTGGTAATTAACTGAGCTTTTGAGTCTGACACTTGGCTTGGAAAGGTTTGC[G/C]
ACAACTTTGAAATTGTGGACAGTAGTCTAAATCTCAAGATGTGCTCAACTTTGAAATATTGTCAACTGTGACTAAAGTCCAGAATCCTTGATAGCAGCTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.80% 36.00% 0.06% 0.15% NA
All Indica  2759 97.90% 1.70% 0.11% 0.22% NA
All Japonica  1512 2.10% 97.90% 0.00% 0.00% NA
Aus  269 59.10% 40.90% 0.00% 0.00% NA
Indica I  595 99.50% 0.00% 0.00% 0.50% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.10% 0.80% 0.11% 0.00% NA
Indica Intermediate  786 94.40% 5.00% 0.25% 0.38% NA
Temperate Japonica  767 1.20% 98.80% 0.00% 0.00% NA
Tropical Japonica  504 2.80% 97.20% 0.00% 0.00% NA
Japonica Intermediate  241 3.30% 96.70% 0.00% 0.00% NA
VI/Aromatic  96 83.30% 16.70% 0.00% 0.00% NA
Intermediate  90 46.70% 52.20% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0135925002 C -> G LOC_Os01g62080.1 3_prime_UTR_variant ; 693.0bp to feature; MODIFIER silent_mutation Average:67.072; most accessible tissue: Callus, score: 85.301 N N N N
vg0135925002 C -> G LOC_Os01g62080.2 3_prime_UTR_variant ; 693.0bp to feature; MODIFIER silent_mutation Average:67.072; most accessible tissue: Callus, score: 85.301 N N N N
vg0135925002 C -> G LOC_Os01g62070.1 upstream_gene_variant ; 3033.0bp to feature; MODIFIER silent_mutation Average:67.072; most accessible tissue: Callus, score: 85.301 N N N N
vg0135925002 C -> G LOC_Os01g62070.2 upstream_gene_variant ; 3033.0bp to feature; MODIFIER silent_mutation Average:67.072; most accessible tissue: Callus, score: 85.301 N N N N
vg0135925002 C -> G LOC_Os01g62070.3 upstream_gene_variant ; 3033.0bp to feature; MODIFIER silent_mutation Average:67.072; most accessible tissue: Callus, score: 85.301 N N N N
vg0135925002 C -> DEL N N silent_mutation Average:67.072; most accessible tissue: Callus, score: 85.301 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0135925002 NA 1.45E-41 mr1089 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
vg0135925002 NA 1.80E-49 mr1125 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
vg0135925002 NA 5.57E-21 mr1163 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
vg0135925002 NA 2.64E-26 mr1251 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
vg0135925002 NA 4.49E-19 mr1253 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
vg0135925002 NA 2.25E-25 mr1411 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
vg0135925002 NA 6.69E-38 mr1435 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
vg0135925002 NA 3.37E-20 mr1541 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
vg0135925002 NA 7.46E-52 mr1599 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
vg0135925002 NA 5.14E-28 mr1793 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
vg0135925002 NA 1.65E-34 mr1828 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
vg0135925002 NA 9.90E-64 mr1125_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
vg0135925002 NA 2.64E-36 mr1223_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
vg0135925002 NA 2.06E-36 mr1251_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
vg0135925002 NA 3.18E-24 mr1350_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
vg0135925002 NA 1.30E-36 mr1435_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
vg0135925002 NA 6.74E-50 mr1480_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
vg0135925002 NA 2.76E-09 mr1506_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
vg0135925002 NA 1.75E-21 mr1968_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
vg0135925002 NA 3.47E-12 mr1986_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