Search for Variation information by Variation ID:
Detailed information for vg0143001311:
| Variant ID: vg0143001311 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 43001311 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTCGCCCAGGGCAACCTCCTTGACCGGGACCTCGTCGCCTGTGATCATCCGCTGCCTCGGGGTGGCGGGGGCGGAGGCGCCAAGCCTCTCGTCGCCACCC[T/C]
CGGGCTTGGACGCAGCGGCGAGGTGGTCCGCGCGCTGCTCCAGACAAGCGAGCGCGACTTTGAGGTCGCCATGGACAGAGATGGGGCCACCGGGGCCCGG
Reverse complement sequence
CCGGGCCCCGGTGGCCCCATCTCTGTCCATGGCGACCTCAAAGTCGCGCTCGCTTGTCTGGAGCAGCGCGCGGACCACCTCGCCGCTGCGTCCAAGCCCG[A/G]
GGGTGGCGACGAGAGGCTTGGCGCCTCCGCCCCCGCCACCCCGAGGCAGCGGATGATCACAGGCGACGAGGTCCCGGTCAAGGAGGTTGCCCTGGGCGAC
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 | 10.20% | 0.30% | 10.43% | 79.05% | NA |
| All Indica | 2759 | 5.10% | 0.40% | 11.53% | 83.04% | NA |
| All Japonica | 1512 | 20.80% | 0.20% | 3.90% | 75.13% | NA |
| Aus | 269 | 4.80% | 0.00% | 30.86% | 64.31% | NA |
| Indica I | 595 | 7.40% | 0.00% | 3.87% | 88.74% | NA |
| Indica II | 465 | 1.90% | 0.90% | 5.59% | 91.61% | NA |
| Indica III | 913 | 3.90% | 0.50% | 19.82% | 75.68% | NA |
| Indica Intermediate | 786 | 6.50% | 0.10% | 11.20% | 82.19% | NA |
| Temperate Japonica | 767 | 38.70% | 0.10% | 0.91% | 60.23% | NA |
| Tropical Japonica | 504 | 1.40% | 0.40% | 8.53% | 89.68% | NA |
| Japonica Intermediate | 241 | 4.10% | 0.00% | 3.73% | 92.12% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 23.96% | 75.00% | NA |
| Intermediate | 90 | 17.80% | 0.00% | 11.11% | 71.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0143001311 | T -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:14.931; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0143001311 | T -> C | LOC_Os01g74230.1 | missense_variant ; p.Glu588Gly; MODERATE | nonsynonymous_codon ; E588G | Average:14.931; most accessible tissue: Zhenshan97 panicle, score: 32.308 | benign  |
0.136 |
DELETERIOUS | 0.01 |