Search for Variation information by Variation ID:
Detailed information for vg1218480412:
| Variant ID: vg1218480412 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18480412 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTTGTGATCAAAAATCCGCCGATTCCTCTCTTTCCAAATTTCCCAGACGACTAACAGAATGAGCGATCGAAGTCCTTTTTTCGGGACACTAGGCGTGTTT[G/A]
CAATGTTCTCCCACCACTGTTTGACTGACTGGGCTTCCTCCCATTCCGTTGGGTCCATCTGCTGATAGCCCACCCATGCAGAGACGAGGTGCCAGATCCT
Reverse complement sequence
AGGATCTGGCACCTCGTCTCTGCATGGGTGGGCTATCAGCAGATGGACCCAACGGAATGGGAGGAAGCCCAGTCAGTCAAACAGTGGTGGGAGAACATTG[C/T]
AAACACGCCTAGTGTCCCGAAAAAAGGACTTCGATCGCTCATTCTGTTAGTCGTCTGGGAAATTTGGAAAGAGAGGAATCGGCGGATTTTTGATCACAAA
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 | 37.20% | 0.30% | 12.42% | 50.02% | NA |
| All Indica | 2759 | 31.50% | 0.50% | 16.56% | 51.43% | NA |
| All Japonica | 1512 | 39.60% | 0.00% | 3.37% | 57.08% | NA |
| Aus | 269 | 74.00% | 0.00% | 16.73% | 9.29% | NA |
| Indica I | 595 | 15.50% | 0.70% | 19.83% | 64.03% | NA |
| Indica II | 465 | 22.40% | 0.00% | 13.98% | 63.66% | NA |
| Indica III | 913 | 48.10% | 0.80% | 16.10% | 35.05% | NA |
| Indica Intermediate | 786 | 29.60% | 0.50% | 16.16% | 53.69% | NA |
| Temperate Japonica | 767 | 60.90% | 0.00% | 1.30% | 37.81% | NA |
| Tropical Japonica | 504 | 12.30% | 0.00% | 6.55% | 81.15% | NA |
| Japonica Intermediate | 241 | 28.60% | 0.00% | 3.32% | 68.05% | NA |
| VI/Aromatic | 96 | 47.90% | 0.00% | 23.96% | 28.12% | NA |
| Intermediate | 90 | 54.40% | 0.00% | 12.22% | 33.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218480412 | G -> DEL | LOC_Os12g30780.1 | N | frameshift_variant | Average:6.918; most accessible tissue: Minghui63 young leaf, score: 11.521 | N | N | N | N |
| vg1218480412 | G -> A | LOC_Os12g30780.1 | missense_variant ; p.Ala200Val; MODERATE | nonsynonymous_codon ; A200V | Average:6.918; most accessible tissue: Minghui63 young leaf, score: 11.521 | possibly damaging  |
1.768 |
TOLERATED | 0.15 |