Search for Variation information by Variation ID:
Detailed information for vg0409515203:
| Variant ID: vg0409515203 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9515203 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACACTTGGGTAATACTTCTTCAAGTATTTGCCATTGAGCGCCCATCCATAAACCTCACCATCAAGCCCTTGCAACATATATGCCCCTTTAGACACAACAT[T/G]
ATAGATTTGAAACGGTCCTTCCCAATTTGGTGACCACTTGCCGAACTTGTTATCCCGAGTTCCAATCGGCAAAATCAACTTCCATACAAGTTCACCTTCC
Reverse complement sequence
GGAAGGTGAACTTGTATGGAAGTTGATTTTGCCGATTGGAACTCGGGATAACAAGTTCGGCAAGTGGTCACCAAATTGGGAAGGACCGTTTCAAATCTAT[A/C]
ATGTTGTGTCTAAAGGGGCATATATGTTGCAAGGGCTTGATGGTGAGGTTTATGGATGGGCGCTCAATGGCAAATACTTGAAGAAGTATTACCCAAGTGT
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 | 90.60% | 0.10% | 0.40% | 8.87% | NA |
| All Indica | 2759 | 99.70% | 0.10% | 0.18% | 0.00% | NA |
| All Japonica | 1512 | 73.30% | 0.00% | 0.66% | 25.99% | NA |
| Aus | 269 | 98.50% | 0.70% | 0.74% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.00% | 0.43% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.20% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 31.50% | 0.00% | 1.59% | 66.87% | NA |
| Japonica Intermediate | 241 | 80.50% | 0.00% | 0.83% | 18.67% | NA |
| VI/Aromatic | 96 | 71.90% | 0.00% | 2.08% | 26.04% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515203 | T -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:35.86; most accessible tissue: Minghui63 young leaf, score: 56.213 | N | N | N | N |
| vg0409515203 | T -> G | LOC_Os04g17380.1 | missense_variant ; p.Asn135His; MODERATE | nonsynonymous_codon | Average:35.86; most accessible tissue: Minghui63 young leaf, score: 56.213 | probably damaging  |
2.123 |
DELETERIOUS | 0.00 |