Search for Variation information by Variation ID:
Detailed information for vg0414145962:
| Variant ID: vg0414145962 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 14145962 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTCCAAGTAGTCGAGGTCATCTCTACGAAGCTGATCTTGATCAACCTCACAGTACATGGTGGCCCCAGGAGAACACAGGGAGAGCTCGGATGGGAGAACC[T/G]
CTTCTGCGCCGTAGACGAGGAAGAAAGGCGTTTCCCCGGTTGCTCGGCTTGGTGTGGTTCGGTTCGCCCAGAGCACCGCTGGCAACTCCTCGATCCATGA
Reverse complement sequence
TCATGGATCGAGGAGTTGCCAGCGGTGCTCTGGGCGAACCGAACCACACCAAGCCGAGCAACCGGGGAAACGCCTTTCTTCCTCGTCTACGGCGCAGAAG[A/C]
GGTTCTCCCATCCGAGCTCTCCCTGTGTTCTCCTGGGGCCACCATGTACTGTGAGGTTGATCAAGATCAGCTTCGTAGAGATGACCTCGACTACTTGGAA
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 22.60% | 0.20% | 10.05% | 67.14% | NA |
| All Indica | 2759 | 10.80% | 0.10% | 0.76% | 88.33% | NA |
| All Japonica | 1512 | 48.80% | 0.30% | 29.03% | 21.83% | NA |
| Aus | 269 | 3.00% | 0.00% | 0.37% | 96.65% | NA |
| Indica I | 595 | 33.60% | 0.30% | 1.18% | 64.87% | NA |
| Indica II | 465 | 3.00% | 0.00% | 0.43% | 96.56% | NA |
| Indica III | 913 | 2.10% | 0.10% | 0.44% | 97.37% | NA |
| Indica Intermediate | 786 | 8.30% | 0.00% | 1.02% | 90.71% | NA |
| Temperate Japonica | 767 | 83.20% | 0.70% | 4.17% | 11.99% | NA |
| Tropical Japonica | 504 | 4.20% | 0.00% | 69.25% | 26.59% | NA |
| Japonica Intermediate | 241 | 32.80% | 0.00% | 24.07% | 43.15% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 1.04% | 89.58% | NA |
| Intermediate | 90 | 18.90% | 0.00% | 14.44% | 66.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0414145962 | T -> DEL | LOC_Os04g24640.1 | N | frameshift_variant | Average:10.323; most accessible tissue: Zhenshan97 root, score: 25.639 | N | N | N | N |
| vg0414145962 | T -> G | LOC_Os04g24640.1 | missense_variant ; p.Glu381Ala; MODERATE | nonsynonymous_codon ; E381A | Average:10.323; most accessible tissue: Zhenshan97 root, score: 25.639 | benign  |
-0.923 |
TOLERATED | 1.00 |