Search for Variation information by Variation ID:
Detailed information for vg0131449516:
| Variant ID: vg0131449516 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31449516 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTCACCTGGGCGCGGATATGTGCCTTGAAAGTTCATGGTGAACTGTTGGCACAAATCCTCCCAAGAGTGGACAGACGCGGGTGGCAAGTTCATTAGCCAA[C/T]
CCCGCGCCTGTCCTTTCAGGGCCATGAGAAAGAAATTCGCCATGACCCTGTCGTCACCCCCGGCGGCCTCGATCCCGGTCGTGTAGACCTGGAGAAACTC
Reverse complement sequence
GAGTTTCTCCAGGTCTACACGACCGGGATCGAGGCCGCCGGGGGTGACGACAGGGTCATGGCGAATTTCTTTCTCATGGCCCTGAAAGGACAGGCGCGGG[G/A]
TTGGCTAATGAACTTGCCACCCGCGTCTGTCCACTCTTGGGAGGATTTGTGCCAACAGTTCACCATGAACTTTCAAGGCACATATCCGCGCCCAGGTGAG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 30.60% | 0.90% | 0.85% | 67.67% | NA |
| All Indica | 2759 | 2.60% | 0.00% | 1.27% | 96.05% | NA |
| All Japonica | 1512 | 80.70% | 2.40% | 0.20% | 16.73% | NA |
| Aus | 269 | 1.10% | 0.00% | 0.37% | 98.51% | NA |
| Indica I | 595 | 4.00% | 0.00% | 2.52% | 93.45% | NA |
| Indica II | 465 | 1.10% | 0.00% | 0.65% | 98.28% | NA |
| Indica III | 913 | 0.50% | 0.10% | 0.11% | 99.23% | NA |
| Indica Intermediate | 786 | 5.00% | 0.00% | 2.04% | 93.00% | NA |
| Temperate Japonica | 767 | 87.70% | 0.00% | 0.13% | 12.13% | NA |
| Tropical Japonica | 504 | 83.10% | 6.90% | 0.20% | 9.72% | NA |
| Japonica Intermediate | 241 | 53.10% | 0.40% | 0.41% | 46.06% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 64.40% | 5.60% | 1.11% | 28.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131449516 | C -> T | LOC_Os01g54660.1 | missense_variant ; p.Gly286Asp; MODERATE | nonsynonymous_codon ; G286D | Average:18.396; most accessible tissue: Zhenshan97 root, score: 46.166 | benign  |
0.866 |
DELETERIOUS | 0.01 |
| vg0131449516 | C -> DEL | LOC_Os01g54660.1 | N | frameshift_variant | Average:18.396; most accessible tissue: Zhenshan97 root, score: 46.166 | N | N | N | N |