Search for Variation information by Variation ID:
Detailed information for vg0409515206:
| Variant ID: vg0409515206 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9515206 |
| Reference Allele: A | Alternative Allele: C,T |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTTGGGTAATACTTCTTCAAGTATTTGCCATTGAGCGCCCATCCATAAACCTCACCATCAAGCCCTTGCAACATATATGCCCCTTTAGACACAACATTAT[A/C,T]
GATTTGAAACGGTCCTTCCCAATTTGGTGACCACTTGCCGAACTTGTTATCCCGAGTTCCAATCGGCAAAATCAACTTCCATACAAGTTCACCTTCCGAA
Reverse complement sequence
TTCGGAAGGTGAACTTGTATGGAAGTTGATTTTGCCGATTGGAACTCGGGATAACAAGTTCGGCAAGTGGTCACCAAATTGGGAAGGACCGTTTCAAATC[T/G,A]
ATAATGTTGTGTCTAAAGGGGCATATATGTTGCAAGGGCTTGATGGTGAGGTTTATGGATGGGCGCTCAATGGCAAATACTTGAAGAAGTATTACCCAAG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.40% | 0.40% | 0.38% | 8.80% | T: 0.02% |
| All Indica | 2759 | 99.30% | 0.50% | 0.14% | 0.00% | T: 0.04% |
| All Japonica | 1512 | 73.30% | 0.10% | 0.79% | 25.79% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.20% | 0.17% | 0.00% | T: 0.17% |
| Indica II | 465 | 98.90% | 0.60% | 0.43% | 0.00% | NA |
| Indica III | 913 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.40% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 31.50% | 0.20% | 1.79% | 66.47% | NA |
| Japonica Intermediate | 241 | 80.50% | 0.00% | 1.24% | 18.26% | NA |
| VI/Aromatic | 96 | 71.90% | 1.00% | 1.04% | 26.04% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 1.11% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515206 | A -> C | LOC_Os04g17380.1 | missense_variant ; p.Tyr134Asp; MODERATE | nonsynonymous_codon ; Y134D | Average:36.07; most accessible tissue: Minghui63 young leaf, score: 56.213 | possibly damaging  |
1.931 |
TOLERATED | 0.21 |
| vg0409515206 | A -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:36.07; most accessible tissue: Minghui63 young leaf, score: 56.213 | N | N | N | N |
| vg0409515206 | A -> T | LOC_Os04g17380.1 | missense_variant ; p.Tyr134Asn; MODERATE | nonsynonymous_codon ; Y134N | Average:36.07; most accessible tissue: Minghui63 young leaf, score: 56.213 | possibly damaging |
1.785 |
TOLERATED | 0.30 |