Search for Variation information by Variation ID:
Detailed information for vg0317761940:
| Variant ID: vg0317761940 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 17761940 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TAGCGCTAACAATGGGAACAGGAATAGCGCTAACAGCAGTAGCAGGAGGAGAAGATTATACCCCGAGAATGGCCCTCCGCTGGATGGTGAGGCAGAATTG[C/T]
CTCCGTTGTTGTAGTCGTTCACGGCACCTCCTCCTGGCGCACCAGCTCCGGATCCGGATCCAGATCCAGCTCCTGTCGGCGGCGGCGTACCACCTCCGCC
Reverse complement sequence
GGCGGAGGTGGTACGCCGCCGCCGACAGGAGCTGGATCTGGATCCGGATCCGGAGCTGGTGCGCCAGGAGGAGGTGCCGTGAACGACTACAACAACGGAG[G/A]
CAATTCTGCCTCACCATCCAGCGGAGGGCCATTCTCGGGGTATAATCTTCTCCTCCTGCTACTGCTGTTAGCGCTATTCCTGTTCCCATTGTTAGCGCTA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 36.40% | 0.30% | 13.50% | 49.87% | NA |
| All Indica | 2759 | 10.90% | 0.20% | 21.82% | 67.13% | NA |
| All Japonica | 1512 | 84.30% | 0.50% | 0.46% | 14.68% | NA |
| Aus | 269 | 3.30% | 0.00% | 6.69% | 89.96% | NA |
| Indica I | 595 | 4.20% | 0.00% | 10.42% | 85.38% | NA |
| Indica II | 465 | 11.20% | 0.90% | 16.34% | 71.61% | NA |
| Indica III | 913 | 14.70% | 0.00% | 33.73% | 51.59% | NA |
| Indica Intermediate | 786 | 11.30% | 0.10% | 19.85% | 68.70% | NA |
| Temperate Japonica | 767 | 98.30% | 1.00% | 0.52% | 0.13% | NA |
| Tropical Japonica | 504 | 63.10% | 0.00% | 0.40% | 36.51% | NA |
| Japonica Intermediate | 241 | 84.20% | 0.00% | 0.41% | 15.35% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 3.12% | 10.42% | NA |
| Intermediate | 90 | 56.70% | 0.00% | 8.89% | 34.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317761940 | C -> T | LOC_Os03g31190.1 | missense_variant ; p.Gly43Asp; MODERATE | nonsynonymous_codon ; G43D | Average:5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 | benign  |
0.232 |
TOLERATED | 0.06 |
| vg0317761940 | C -> DEL | LOC_Os03g31190.1 | N | frameshift_variant | Average:5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 | N | N | N | N |