Search for Variation information by Variation ID:
Detailed information for vg0427368731:
| Variant ID: vg0427368731 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 27368731 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 59. )
Flanking Sequence (100 bp) in Reference Genome:
GGTTCATCAAGTGACAAGTAATAATTTTCGTCCGGCTTTGTCCTATAAAACCATTTCTCATCTATATACACAATGTTGTACAAAGATTTGAAAGTTGGCT[T/C]
GTCCGGTATGCTTTGGCTATCAAGCATTTGTATGCAAAATTGCACACGGGCCTTCATGTTATCTTCGGTCAAGGTGAACTTTATGGCATTTGTATGGCGC
Reverse complement sequence
GCGCCATACAAATGCCATAAAGTTCACCTTGACCGAAGATAACATGAAGGCCCGTGTGCAATTTTGCATACAAATGCTTGATAGCCAAAGCATACCGGAC[A/G]
AGCCAACTTTCAAATCTTTGTACAACATTGTGTATATAGATGAGAAATGGTTTTATAGGACAAAGCCGGACGAAAATTATTACTTGTCACTTGATGAACC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.30% | 0.60% | 32.33% | 2.75% | NA |
| All Indica | 2759 | 39.70% | 0.90% | 54.62% | 4.71% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.33% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 25.20% | 0.50% | 65.88% | 8.40% | NA |
| Indica II | 465 | 14.60% | 1.30% | 76.13% | 7.96% | NA |
| Indica III | 913 | 55.00% | 1.40% | 41.51% | 2.08% | NA |
| Indica Intermediate | 786 | 47.80% | 0.50% | 48.60% | 3.05% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 81.10% | 1.10% | 17.78% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0427368731 | T -> C | LOC_Os04g46210.1 | missense_variant ; p.Lys179Glu; MODERATE | nonsynonymous_codon ; K179E | Average:24.665; most accessible tissue: Zhenshan97 root, score: 39.742 | benign  |
-1.441 |
TOLERATED | 1.00 |
| vg0427368731 | T -> DEL | LOC_Os04g46210.1 | N | frameshift_variant | Average:24.665; most accessible tissue: Zhenshan97 root, score: 39.742 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0427368731 | 2.60E-06 | 2.37E-06 | mr1530 | 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 |
| vg0427368731 | NA | 1.34E-08 | mr1770 | 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 |
| vg0427368731 | NA | 9.25E-09 | mr1172_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 |
| vg0427368731 | NA | 2.68E-09 | mr1690_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 |