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Detailed information for vg0435372935:

Variant ID: vg0435372935 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 35372935
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: 331. )

Flanking Sequence (100 bp) in Reference Genome:


AGCATGCATATCAAAACTATATTGTGTCCATATCTATGTGTCAACTACTTGTTCTTATTCTTAAAATTTCAGTAGTTCGTTATGCTCACATTTTATTAGG[C/T]
GTCATCCATCTGATTTTAAATAAACTATCATCAGCTGCGATATAGGCAGTAGTTTCTTTTATGTTGATTAATGCTTTATTGAAGTTGTAACTATGGTGCA

Reverse complement sequence

TGCACCATAGTTACAACTTCAATAAAGCATTAATCAACATAAAAGAAACTACTGCCTATATCGCAGCTGATGATAGTTTATTTAAAATCAGATGGATGAC[G/A]
CCTAATAAAATGTGAGCATAACGAACTACTGAAATTTTAAGAATAAGAACAAGTAGTTGACACATAGATATGGACACAATATAGTTTTGATATGCATGCT

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 97.30% 2.30% 0.38% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 91.90% 6.90% 1.12% 0.00% NA
Aus  269 100.00% 0.00% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 77.80% 19.60% 2.58% 0.00% NA
Japonica Intermediate  241 96.70% 2.10% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 3.30% 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
vg0435372935 C -> T LOC_Os04g59494.1 intron_variant ; MODIFIER silent_mutation Average:51.852; most accessible tissue: Callus, score: 79.699 N N N N
vg0435372935 C -> T LOC_Os04g59494.4 intron_variant ; MODIFIER silent_mutation Average:51.852; most accessible tissue: Callus, score: 79.699 N N N N
vg0435372935 C -> T LOC_Os04g59494.2 intron_variant ; MODIFIER silent_mutation Average:51.852; most accessible tissue: Callus, score: 79.699 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0435372935 NA 7.93E-06 mr1073 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
vg0435372935 9.12E-06 9.11E-06 mr1601 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
vg0435372935 NA 6.84E-07 mr1830 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
vg0435372935 1.74E-06 NA mr1082_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
vg0435372935 6.47E-07 NA mr1083_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
vg0435372935 3.29E-06 NA mr1103_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
vg0435372935 3.40E-06 NA mr1104_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
vg0435372935 2.17E-06 NA mr1107_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
vg0435372935 4.67E-06 NA mr1155_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
vg0435372935 1.83E-07 NA mr1226_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
vg0435372935 3.12E-06 NA mr1408_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