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Detailed information for vg0130078302:

Variant ID: vg0130078302 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 30078302
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCAAATGGGGGCGTCGGAAAAAATGCAATGGGGCAGCCAGGAAGAATAGAACACGCAACCTAAGATTTGCGTGCGTGCGCCTTCACAAGTGAACCAGCA[C/T]
CTCGTTTTGATTTCTTCTGTACAAGTTATATACCGGTTACAATATAACTACGTACAAGTTATATATCGGTTACAATATAACTATAATCAAGTTATAATGT

Reverse complement sequence

ACATTATAACTTGATTATAGTTATATTGTAACCGATATATAACTTGTACGTAGTTATATTGTAACCGGTATATAACTTGTACAGAAGAAATCAAAACGAG[G/A]
TGCTGGTTCACTTGTGAAGGCGCACGCACGCAAATCTTAGGTTGCGTGTTCTATTCTTCCTGGCTGCCCCATTGCATTTTTTCCGACGCCCCCATTTGCA

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 93.20% 6.80% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 85.80% 14.20% 0.00% 0.00% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 99.10% 0.90% 0.00% 0.00% NA
Tropical Japonica  504 63.10% 36.90% 0.00% 0.00% NA
Japonica Intermediate  241 90.90% 9.10% 0.00% 0.00% NA
VI/Aromatic  96 21.90% 78.10% 0.00% 0.00% NA
Intermediate  90 75.60% 24.40% 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
vg0130078302 C -> T LOC_Os01g52340.1 upstream_gene_variant ; 1347.0bp to feature; MODIFIER silent_mutation Average:40.374; most accessible tissue: Callus, score: 84.5 N N N N
vg0130078302 C -> T LOC_Os01g52330.1 downstream_gene_variant ; 1176.0bp to feature; MODIFIER silent_mutation Average:40.374; most accessible tissue: Callus, score: 84.5 N N N N
vg0130078302 C -> T LOC_Os01g52330-LOC_Os01g52340 intergenic_region ; MODIFIER silent_mutation Average:40.374; most accessible tissue: Callus, score: 84.5 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0130078302 NA 1.32E-10 mr1070 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
vg0130078302 NA 5.80E-06 mr1129_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
vg0130078302 NA 6.02E-07 mr1250_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
vg0130078302 NA 7.57E-06 mr1438_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
vg0130078302 NA 3.90E-06 mr1553_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
vg0130078302 5.58E-07 5.58E-07 mr1574_2 Jap_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
vg0130078302 NA 5.76E-06 mr1781_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