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Detailed information for vg0135985611:

Variant ID: vg0135985611 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35985611
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


AGGGAACTTGAAAGCATAAAAGGGAAAATTCAGATATATTGAAATTCAAAGAATTCGATTCGTTCTCCTCATATTGAAATTAGAAGGGCAGAGGAAGAAA[C/T]
GGGGTAAACCTTATGATAGCAAATTTAACAGAAGAGATTCAAATCTAATAGAACATGGTCCACAAGTGTCGAGAACAGAAAATGAACAATACTAGCAATA

Reverse complement sequence

TATTGCTAGTATTGTTCATTTTCTGTTCTCGACACTTGTGGACCATGTTCTATTAGATTTGAATCTCTTCTGTTAAATTTGCTATCATAAGGTTTACCCC[G/A]
TTTCTTCCTCTGCCCTTCTAATTTCAATATGAGGAGAACGAATCGAATTCTTTGAATTTCAATATATCTGAATTTTCCCTTTTATGCTTTCAAGTTCCCT

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 52.30% 47.50% 0.15% 0.00% NA
All Indica  2759 26.50% 73.30% 0.22% 0.00% NA
All Japonica  1512 98.10% 1.90% 0.00% 0.00% NA
Aus  269 41.60% 58.40% 0.00% 0.00% NA
Indica I  595 11.10% 88.60% 0.34% 0.00% NA
Indica II  465 6.20% 93.80% 0.00% 0.00% NA
Indica III  913 40.70% 59.30% 0.00% 0.00% NA
Indica Intermediate  786 33.70% 65.80% 0.51% 0.00% NA
Temperate Japonica  767 98.70% 1.30% 0.00% 0.00% NA
Tropical Japonica  504 97.20% 2.80% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 7.30% 1.04% 0.00% NA
Intermediate  90 65.60% 34.40% 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
vg0135985611 C -> T LOC_Os01g62160.1 intron_variant ; MODIFIER silent_mutation Average:33.26; most accessible tissue: Minghui63 root, score: 41.911 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0135985611 NA 2.48E-10 mr1078 Ind_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
vg0135985611 NA 2.78E-07 mr1096 Ind_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
vg0135985611 NA 3.17E-09 mr1133 Ind_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
vg0135985611 NA 3.17E-21 mr1155 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
vg0135985611 NA 2.04E-09 mr1887 Ind_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
vg0135985611 NA 1.00E-07 mr1078_2 Ind_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
vg0135985611 NA 6.06E-08 mr1133_2 Ind_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
vg0135985611 NA 7.29E-06 mr1428_2 Ind_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
vg0135985611 NA 7.89E-07 mr1870_2 Ind_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