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Detailed information for vg0630442875:

Variant ID: vg0630442875 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 30442875
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.02, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TTGCCGATGGAATATATCCCGAGTGGGCTGCCTTCGTGAAGACAATAAGAAAACCTCAAACGGAGAAACATAAATTATATGCACAACGACAAGAAGGGGC[C/A]
AGAAAGGATGTCGAGTGTGCATTTGGCGTGTTGCAATCCCGTTTTGATATTGTCAACCGTCCAGCACGGTTGTGGAAAAGGAATGATGTTGTTAATATAA

Reverse complement sequence

TTATATTAACAACATCATTCCTTTTCCACAACCGTGCTGGACGGTTGACAATATCAAAACGGGATTGCAACACGCCAAATGCACACTCGACATCCTTTCT[G/T]
GCCCCTTCTTGTCGTTGTGCATATAATTTATGTTTCTCCGTTTGAGGTTTTCTTATTGTCTTCACGAAGGCAGCCCACTCGGGATATATTCCATCGGCAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 39.10% 6.10% 2.01% 52.88% NA
All Indica  2759 21.10% 9.20% 2.61% 67.16% NA
All Japonica  1512 63.40% 1.10% 0.93% 34.59% NA
Aus  269 89.60% 4.50% 0.37% 5.58% NA
Indica I  595 45.00% 1.70% 3.19% 50.08% NA
Indica II  465 7.10% 1.50% 2.58% 88.82% NA
Indica III  913 12.50% 16.90% 1.53% 69.11% NA
Indica Intermediate  786 21.10% 10.40% 3.44% 65.01% NA
Temperate Japonica  767 94.00% 0.00% 0.00% 6.00% NA
Tropical Japonica  504 18.80% 3.00% 2.38% 75.79% NA
Japonica Intermediate  241 59.30% 0.40% 0.83% 39.42% NA
VI/Aromatic  96 36.50% 1.00% 3.12% 59.38% NA
Intermediate  90 33.30% 4.40% 5.56% 56.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0630442875 C -> A LOC_Os06g50290.1 synonymous_variant ; p.Ala783Ala; LOW synonymous_codon Average:10.229; most accessible tissue: Callus, score: 19.121 N N N N
vg0630442875 C -> DEL LOC_Os06g50290.1 N frameshift_variant Average:10.229; most accessible tissue: Callus, score: 19.121 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0630442875 NA 5.42E-06 mr1064_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
vg0630442875 6.94E-07 NA mr1124_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
vg0630442875 NA 9.91E-06 mr1312_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
vg0630442875 NA 2.16E-06 mr1363_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
vg0630442875 NA 3.31E-06 mr1663_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
vg0630442875 NA 5.37E-06 mr1923_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