Search for Variation information by Variation ID:
Detailed information for vg0402111251:
| Variant ID: vg0402111251 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2111251 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, T: 0.13, others allele: 0.00, population size: 63. )
Flanking Sequence (100 bp) in Reference Genome:
AACATACTTTCCTTCTCTGCCTTGCTAAGAGTGTAGCTGGCTGGACTCAAGTAATGGCTGCCTTTCTCCTGTGGTTCCGGGTGAAGGTCGCCGCGTTGTT[T/C]
CATATGCTTCAGATCATTACGTGCTTCCAGTGTATCTTTCAACTTTCCATATACACCTAGGAAGCCAAGAAGGTTTACGAAAAGGTTCTTAGTGAGGTGC
Reverse complement sequence
GCACCTCACTAAGAACCTTTTCGTAAACCTTCTTGGCTTCCTAGGTGTATATGGAAAGTTGAAAGATACACTGGAAGCACGTAATGATCTGAAGCATATG[A/G]
AACAACGCGGCGACCTTCACCCGGAACCACAGGAGAAAGGCAGCCATTACTTGAGTCCAGCCAGCTACACTCTTAGCAAGGCAGAGAAGGAAAGTATGTT
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 | 25.50% | 17.40% | 24.19% | 32.92% | NA |
| All Indica | 2759 | 21.10% | 17.50% | 33.38% | 28.02% | NA |
| All Japonica | 1512 | 39.00% | 15.90% | 8.07% | 37.10% | NA |
| Aus | 269 | 4.80% | 10.40% | 19.70% | 65.06% | NA |
| Indica I | 595 | 28.90% | 10.40% | 35.80% | 24.87% | NA |
| Indica II | 465 | 24.30% | 5.80% | 25.59% | 44.30% | NA |
| Indica III | 913 | 15.40% | 27.80% | 36.80% | 19.93% | NA |
| Indica Intermediate | 786 | 20.00% | 17.70% | 32.19% | 30.15% | NA |
| Temperate Japonica | 767 | 69.10% | 15.40% | 4.56% | 10.95% | NA |
| Tropical Japonica | 504 | 4.20% | 18.30% | 14.29% | 63.29% | NA |
| Japonica Intermediate | 241 | 15.80% | 12.40% | 6.22% | 65.56% | NA |
| VI/Aromatic | 96 | 1.00% | 54.20% | 25.00% | 19.79% | NA |
| Intermediate | 90 | 23.30% | 20.00% | 25.56% | 31.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402111251 | T -> C | LOC_Os04g04430.1 | missense_variant ; p.Lys519Glu; MODERATE | nonsynonymous_codon ; K519E | Average:6.144; most accessible tissue: Callus, score: 13.114 | benign  |
-0.644 |
TOLERATED | 1.00 |
| vg0402111251 | T -> DEL | LOC_Os04g04430.1 | N | frameshift_variant | Average:6.144; most accessible tissue: Callus, score: 13.114 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402111251 | NA | 2.22E-06 | mr1077_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 |
| vg0402111251 | NA | 6.71E-06 | mr1206_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 |
| vg0402111251 | NA | 7.35E-06 | mr1252_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 |
| vg0402111251 | NA | 4.09E-06 | mr1441_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 |
| vg0402111251 | 2.77E-06 | NA | mr1457_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 |
| vg0402111251 | NA | 4.72E-06 | mr1780_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 |