Search for Variation information by Variation ID:
Detailed information for vg1218480317:
| Variant ID: vg1218480317 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18480317 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGTGGGATTAACTCACGCAACCGCTTAGCTCCTGCTAAAGCCCAAAGGCTCGCCTCCTCTTTGATTTTCATTAGTAGGAAGTTCGTTGCCACCTCTTTGT[G/A]
ATCAAAAATCCGCCGATTCCTCTCTTTCCAAATTTCCCAGACGACTAACAGAATGAGCGATCGAAGTCCTTTTTTCGGGACACTAGGCGTGTTTGCAATG
Reverse complement sequence
CATTGCAAACACGCCTAGTGTCCCGAAAAAAGGACTTCGATCGCTCATTCTGTTAGTCGTCTGGGAAATTTGGAAAGAGAGGAATCGGCGGATTTTTGAT[C/T]
ACAAAGAGGTGGCAACGAACTTCCTACTAATGAAAATCAAAGAGGAGGCGAGCCTTTGGGCTTTAGCAGGAGCTAAGCGGTTGCGTGAGTTAATCCCACA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 13.30% | 0.20% | 1.97% | 84.49% | NA |
| All Indica | 2759 | 2.20% | 0.10% | 1.78% | 95.90% | NA |
| All Japonica | 1512 | 35.50% | 0.10% | 0.33% | 64.09% | NA |
| Aus | 269 | 1.10% | 1.90% | 10.04% | 86.99% | NA |
| Indica I | 595 | 2.50% | 0.00% | 0.17% | 97.31% | NA |
| Indica II | 465 | 3.40% | 0.00% | 1.29% | 95.27% | NA |
| Indica III | 913 | 1.00% | 0.20% | 2.41% | 96.39% | NA |
| Indica Intermediate | 786 | 2.50% | 0.30% | 2.54% | 94.66% | NA |
| Temperate Japonica | 767 | 60.40% | 0.00% | 0.13% | 39.50% | NA |
| Tropical Japonica | 504 | 3.00% | 0.20% | 0.60% | 96.23% | NA |
| Japonica Intermediate | 241 | 24.50% | 0.00% | 0.41% | 75.10% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 6.25% | 89.58% | NA |
| Intermediate | 90 | 28.90% | 0.00% | 6.67% | 64.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218480317 | G -> DEL | LOC_Os12g30780.1 | N | frameshift_variant | Average:8.523; most accessible tissue: Callus, score: 21.903 | N | N | N | N |
| vg1218480317 | G -> A | LOC_Os12g30780.1 | missense_variant ; p.His232Tyr; MODERATE | nonsynonymous_codon ; H232Y | Average:8.523; most accessible tissue: Callus, score: 21.903 | possibly damaging  |
1.823 |
TOLERATED | 1.00 |