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Detailed information for vg0206275287:

Variant ID: vg0206275287 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 6275287
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAACTTAATTAATCATATGCTAATAGCTTCTTGTTTTTCATGCCCTTACTTAATATTCATTTTCATTAGTATCAAACACCAGTCGAGTCCCTCGCAAAC[C/T]
GCAGCCCTGCTCAATCAGTTCCCCGCATATCCGCTTACATCACCCACGTCGAGTGGCCTAGGAGATCCGTGCGGTGCACCTCGCTGATGATGGCGCTACT

Reverse complement sequence

AGTAGCGCCATCATCAGCGAGGTGCACCGCACGGATCTCCTAGGCCACTCGACGTGGGTGATGTAAGCGGATATGCGGGGAACTGATTGAGCAGGGCTGC[G/A]
GTTTGCGAGGGACTCGACTGGTGTTTGATACTAATGAAAATGAATATTAAGTAAGGGCATGAAAAACAAGAAGCTATTAGCATATGATTAATTAAGTTTT

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 49.30% 3.70% 1.06% 45.98% NA
All Indica  2759 18.40% 5.80% 1.67% 74.05% NA
All Japonica  1512 98.10% 0.20% 0.13% 1.52% NA
Aus  269 73.60% 0.00% 0.00% 26.39% NA
Indica I  595 2.70% 6.40% 2.02% 88.91% NA
Indica II  465 37.20% 2.60% 2.15% 58.06% NA
Indica III  913 19.20% 6.70% 0.88% 73.27% NA
Indica Intermediate  786 18.40% 6.40% 2.04% 73.16% NA
Temperate Japonica  767 97.70% 0.10% 0.26% 1.96% NA
Tropical Japonica  504 99.40% 0.20% 0.00% 0.40% NA
Japonica Intermediate  241 97.10% 0.40% 0.00% 2.49% NA
VI/Aromatic  96 83.30% 8.30% 1.04% 7.29% NA
Intermediate  90 63.30% 3.30% 1.11% 32.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0206275287 C -> T LOC_Os02g12100.1 missense_variant ; p.Arg97Cys; MODERATE nonsynonymous_codon ; R97C Average:34.3; most accessible tissue: Minghui63 panicle, score: 73.225 unknown unknown DELETERIOUS 0.01
vg0206275287 C -> DEL LOC_Os02g12100.1 N frameshift_variant Average:34.3; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0206275287 NA 1.53E-08 mr1006 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
vg0206275287 NA 7.70E-07 mr1007 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
vg0206275287 NA 1.13E-06 mr1037 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
vg0206275287 NA 8.32E-09 mr1052 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
vg0206275287 NA 3.40E-06 mr1870 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
vg0206275287 NA 2.77E-06 mr1986 Ind_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
vg0206275287 NA 4.79E-06 mr1006_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
vg0206275287 NA 2.89E-06 mr1219_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