Search for Variation information by Variation ID:
Detailed information for vg0128477000:
| Variant ID: vg0128477000 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28477000 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACCCTCCGATGGGATGGGTCATACCAACCTCCACTCCGCCGGAAGCAGGTGCAACGTGGAAGCACGGTTGTTTGCTGATGACGCGACCGGCGTCAGACCA[A/G]
TCACAGACCGGTCATTCTTGTCCTCCACGCGTCAGTTTAGCATGCTACACGTCTGCCCTTCTTCATACAACGACTTCCTTGCAATGGTTGCGATGAAGCC
Reverse complement sequence
GGCTTCATCGCAACCATTGCAAGGAAGTCGTTGTATGAAGAAGGGCAGACGTGTAGCATGCTAAACTGACGCGTGGAGGACAAGAATGACCGGTCTGTGA[T/C]
TGGTCTGACGCCGGTCGCGTCATCAGCAAACAACCGTGCTTCCACGTTGCACCTGCTTCCGGCGGAGTGGAGGTTGGTATGACCCATCCCATCGGAGGGT
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 | 31.60% | 0.00% | 1.14% | 67.22% | NA |
| All Indica | 2759 | 2.80% | 0.00% | 1.41% | 95.76% | NA |
| All Japonica | 1512 | 89.70% | 0.00% | 0.20% | 10.12% | NA |
| Aus | 269 | 1.90% | 0.00% | 3.72% | 94.42% | NA |
| Indica I | 595 | 2.40% | 0.20% | 3.03% | 94.45% | NA |
| Indica II | 465 | 5.40% | 0.00% | 2.37% | 92.26% | NA |
| Indica III | 913 | 1.40% | 0.00% | 0.11% | 98.47% | NA |
| Indica Intermediate | 786 | 3.20% | 0.00% | 1.15% | 95.67% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.13% | 0.52% | NA |
| Tropical Japonica | 504 | 73.20% | 0.00% | 0.20% | 26.59% | NA |
| Japonica Intermediate | 241 | 93.40% | 0.00% | 0.41% | 6.22% | NA |
| VI/Aromatic | 96 | 14.60% | 0.00% | 1.04% | 84.38% | NA |
| Intermediate | 90 | 46.70% | 0.00% | 1.11% | 52.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128477000 | A -> G | LOC_Os01g49500.1 | missense_variant ; p.Ile30Val; MODERATE | nonsynonymous_codon ; I30V | Average:5.966; most accessible tissue: Callus, score: 16.999 | benign  |
-1.092 |
TOLERATED | 1.00 |
| vg0128477000 | A -> DEL | LOC_Os01g49500.1 | N | frameshift_variant | Average:5.966; most accessible tissue: Callus, score: 16.999 | N | N | N | N |