Search for Variation information by Variation ID:
Detailed information for vg0124422057:
| Variant ID: vg0124422057 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 24422057 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCTCGCTGGGTGGCCATACTTCTTCCTCTCTTTTTAGTGAGTGGAAGTTGAGTGGTTTTATTTGGTACCTCTACTCTTTCTGGTGCATTCTGAGCAGGAA[T/C]
GAAAGATTTAGTCACACATTTATAATTGGTAAATGCATCTGGCAGGTTATTTGCAAGTCTTTGCAAATGTATAATTTTCTGAACTTGAAGTTCAATTTCA
Reverse complement sequence
TGAAATTGAACTTCAAGTTCAGAAAATTATACATTTGCAAAGACTTGCAAATAACCTGCCAGATGCATTTACCAATTATAAATGTGTGACTAAATCTTTC[A/G]
TTCCTGCTCAGAATGCACCAGAAAGAGTAGAGGTACCAAATAAAACCACTCAACTTCCACTCACTAAAAAGAGAGGAAGAAGTATGGCCACCCAGCGAGA
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 | 26.80% | 0.60% | 16.17% | 56.43% | NA |
| All Indica | 2759 | 2.20% | 0.80% | 7.18% | 89.85% | NA |
| All Japonica | 1512 | 71.60% | 0.30% | 20.63% | 7.47% | NA |
| Aus | 269 | 1.90% | 1.10% | 88.10% | 8.92% | NA |
| Indica I | 595 | 1.00% | 1.30% | 5.88% | 91.76% | NA |
| Indica II | 465 | 2.20% | 0.90% | 4.09% | 92.90% | NA |
| Indica III | 913 | 2.20% | 0.00% | 8.21% | 89.59% | NA |
| Indica Intermediate | 786 | 3.20% | 1.10% | 8.78% | 86.90% | NA |
| Temperate Japonica | 767 | 98.70% | 0.00% | 0.91% | 0.39% | NA |
| Tropical Japonica | 504 | 37.10% | 0.60% | 44.25% | 18.06% | NA |
| Japonica Intermediate | 241 | 57.30% | 0.80% | 34.02% | 7.88% | NA |
| VI/Aromatic | 96 | 80.20% | 0.00% | 4.17% | 15.62% | NA |
| Intermediate | 90 | 44.40% | 1.10% | 14.44% | 40.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0124422057 | T -> DEL | LOC_Os01g42920.1 | N | frameshift_variant | Average:15.604; most accessible tissue: Callus, score: 24.117 | N | N | N | N |
| vg0124422057 | T -> C | LOC_Os01g42920.1 | missense_variant ; p.Ile320Val; MODERATE | nonsynonymous_codon ; I320V | Average:15.604; most accessible tissue: Callus, score: 24.117 | benign  |
0.874 |
TOLERATED | 0.06 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0124422057 | 3.22E-06 | 3.21E-06 | mr1173 | 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 |
| vg0124422057 | NA | 1.71E-07 | mr1190 | 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 |
| vg0124422057 | NA | 1.10E-13 | mr1874 | 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 |