Search for Variation information by Variation ID:
Detailed information for vg0125112038:
| Variant ID: vg0125112038 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 25112038 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCACGTCATCGGCAGACAACCGAGCTCCCACGTTGCATCTGCTTCCGGCGGAGTGGAGGTAG[A/G]
TATGACCCATCCCATCGGAGGGTCATTCGGACAGCAGCCATTGCAAATCTTCACCCATTAATGAAGGAATGACAGGGAGATCCCCTGTGTCAGGCGAGTG
Reverse complement sequence
CACTCGCCTGACACAGGGGATCTCCCTGTCATTCCTTCATTAATGGGTGAAGATTTGCAATGGCTGCTGTCCGAATGACCCTCCGATGGGATGGGTCATA[T/C]
CTACCTCCACTCCGCCGGAAGCAGATGCAACGTGGGAGCTCGGTTGTCTGCCGATGACGTGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 50.80% | 0.30% | 6.03% | 42.91% | NA |
| All Indica | 2759 | 39.50% | 0.50% | 9.28% | 50.74% | NA |
| All Japonica | 1512 | 74.70% | 0.00% | 0.99% | 24.27% | NA |
| Aus | 269 | 15.60% | 0.00% | 1.49% | 82.90% | NA |
| Indica I | 595 | 33.90% | 0.00% | 15.13% | 50.92% | NA |
| Indica II | 465 | 61.10% | 0.00% | 4.95% | 33.98% | NA |
| Indica III | 913 | 30.20% | 1.30% | 8.54% | 59.91% | NA |
| Indica Intermediate | 786 | 41.70% | 0.10% | 8.27% | 49.87% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.13% | 1.56% | NA |
| Tropical Japonica | 504 | 44.00% | 0.00% | 1.98% | 53.97% | NA |
| Japonica Intermediate | 241 | 63.90% | 0.00% | 1.66% | 34.44% | NA |
| VI/Aromatic | 96 | 85.40% | 1.00% | 1.04% | 12.50% | NA |
| Intermediate | 90 | 61.10% | 0.00% | 10.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0125112038 | A -> G | LOC_Os01g43830.1 | missense_variant ; p.Ile4Thr; MODERATE | nonsynonymous_codon ; I4T | Average:6.081; most accessible tissue: Callus, score: 10.3 | benign  |
-0.472 |
TOLERATED | 1.00 |
| vg0125112038 | A -> DEL | LOC_Os01g43830.1 | N | frameshift_variant | Average:6.081; most accessible tissue: Callus, score: 10.3 | N | N | N | N |