Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0630422637:

Variant ID: vg0630422637 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 30422637
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.07, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


GTTTCTGAAAATGCGGATCCAGATCAAACTATTTCTGAAAATGTTCACAAATTTCAAAAACTAAAGCAAATTACATTGTAAAATACTGGGCGAGCTTCTT[C/T]
TTCTTGACCTGTACTTGTTTACCGAAGCACGCTGACGTCCGGCGTGCCCACTTTCTGATCTTCTTGTCTTCAGCAATGTCGGAAAAATCACAGTGATCAT

Reverse complement sequence

ATGATCACTGTGATTTTTCCGACATTGCTGAAGACAAGAAGATCAGAAAGTGGGCACGCCGGACGTCAGCGTGCTTCGGTAAACAAGTACAGGTCAAGAA[G/A]
AAGAAGCTCGCCCAGTATTTTACAATGTAATTTGCTTTAGTTTTTGAAATTTGTGAACATTTTCAGAAATAGTTTGATCTGGATCCGCATTTTCAGAAAC

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 51.20% 48.60% 0.15% 0.00% NA
All Indica  2759 27.80% 72.00% 0.18% 0.00% NA
All Japonica  1512 88.40% 11.60% 0.00% 0.00% NA
Aus  269 64.70% 35.30% 0.00% 0.00% NA
Indica I  595 29.20% 70.60% 0.17% 0.00% NA
Indica II  465 46.90% 52.90% 0.22% 0.00% NA
Indica III  913 17.60% 82.30% 0.11% 0.00% NA
Indica Intermediate  786 27.40% 72.40% 0.25% 0.00% NA
Temperate Japonica  767 95.60% 4.40% 0.00% 0.00% NA
Tropical Japonica  504 76.80% 23.20% 0.00% 0.00% NA
Japonica Intermediate  241 90.00% 10.00% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 56.70% 41.10% 2.22% 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
vg0630422637 C -> T LOC_Os06g50250.1 synonymous_variant ; p.Lys148Lys; LOW synonymous_codon Average:51.639; most accessible tissue: Zhenshan97 root, score: 75.661 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0630422637 NA 1.89E-09 mr1016 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
vg0630422637 NA 2.71E-10 mr1017 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
vg0630422637 NA 5.73E-10 mr1018 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
vg0630422637 NA 7.02E-11 mr1055 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
vg0630422637 NA 1.71E-10 mr1390 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
vg0630422637 NA 8.73E-12 mr1490 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
vg0630422637 NA 1.72E-12 mr1055_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
vg0630422637 NA 1.02E-13 mr1132_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
vg0630422637 NA 4.78E-13 mr1390_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
vg0630422637 NA 9.11E-14 mr1490_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