Search for Variation information by Variation ID:
Detailed information for vg0409515205:
| Variant ID: vg0409515205 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9515205 |
| Reference Allele: T | Alternative Allele: C,G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACTTGGGTAATACTTCTTCAAGTATTTGCCATTGAGCGCCCATCCATAAACCTCACCATCAAGCCCTTGCAACATATATGCCCCTTTAGACACAACATTA[T/C,G]
AGATTTGAAACGGTCCTTCCCAATTTGGTGACCACTTGCCGAACTTGTTATCCCGAGTTCCAATCGGCAAAATCAACTTCCATACAAGTTCACCTTCCGA
Reverse complement sequence
TCGGAAGGTGAACTTGTATGGAAGTTGATTTTGCCGATTGGAACTCGGGATAACAAGTTCGGCAAGTGGTCACCAAATTGGGAAGGACCGTTTCAAATCT[A/G,C]
TAATGTTGTGTCTAAAGGGGCATATATGTTGCAAGGGCTTGATGGTGAGGTTTATGGATGGGCGCTCAATGGCAAATACTTGAAGAAGTATTACCCAAGT
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 | 90.00% | 0.20% | 0.87% | 8.80% | C: 0.13% |
| All Indica | 2759 | 98.60% | 0.40% | 0.91% | 0.00% | C: 0.11% |
| All Japonica | 1512 | 73.40% | 0.00% | 0.79% | 25.79% | NA |
| Aus | 269 | 98.50% | 0.00% | 0.74% | 0.00% | C: 0.74% |
| Indica I | 595 | 99.70% | 0.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.00% | 0.86% | 0.00% | NA |
| Indica III | 913 | 97.50% | 1.10% | 1.20% | 0.00% | C: 0.22% |
| Indica Intermediate | 786 | 98.90% | 0.00% | 1.02% | 0.00% | C: 0.13% |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 31.70% | 0.00% | 1.79% | 66.47% | NA |
| Japonica Intermediate | 241 | 80.50% | 0.00% | 1.24% | 18.26% | NA |
| VI/Aromatic | 96 | 71.90% | 0.00% | 2.08% | 26.04% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 0.00% | 1.11% | C: 1.11% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515205 | T -> C | LOC_Os04g17380.1 | missense_variant ; p.Tyr134Cys; MODERATE | stop_gained | Average:35.917; most accessible tissue: Minghui63 young leaf, score: 56.213 | N | N | N | N |
| vg0409515205 | T -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:35.917; most accessible tissue: Minghui63 young leaf, score: 56.213 | N | N | N | N |
| vg0409515205 | T -> G | LOC_Os04g17380.1 | missense_variant ; p.Tyr134Ser; MODERATE | nonsynonymous_codon ; Y134S | Average:35.917; most accessible tissue: Minghui63 young leaf, score: 56.213 | possibly damaging  |
1.699 |
TOLERATED | 0.37 |