Search for Variation information by Variation ID:
Detailed information for vg0142999472:
| Variant ID: vg0142999472 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 42999472 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCATTTCACCACCCGTCCTGTACCCTCTTGATTATGCAAGATTTGACCGAGGGGGTAAGACGTAACTACTGTGACCCGATGCGCCTGGAAATAATGGCGC[A/G]
GTTTCCTCGAGGCCATTAGAATAGCGTAAAGCATCTTCTGGGCCTGAGGGTATCGGGTTTTGGCGTCCCGGAGGGCCTCACTAACAAAGTAGACGGGCCG
Reverse complement sequence
CGGCCCGTCTACTTTGTTAGTGAGGCCCTCCGGGACGCCAAAACCCGATACCCTCAGGCCCAGAAGATGCTTTACGCTATTCTAATGGCCTCGAGGAAAC[T/C]
GCGCCATTATTTCCAGGCGCATCGGGTCACAGTAGTTACGTCTTACCCCCTCGGTCAAATCTTGCATAATCAAGAGGGTACAGGACGGGTGGTGAAATGG
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 | 12.60% | 0.70% | 8.93% | 77.78% | NA |
| All Indica | 2759 | 8.80% | 0.70% | 9.82% | 80.75% | NA |
| All Japonica | 1512 | 21.40% | 0.00% | 1.79% | 76.85% | NA |
| Aus | 269 | 3.70% | 5.20% | 34.57% | 56.51% | NA |
| Indica I | 595 | 1.80% | 1.30% | 4.71% | 92.10% | NA |
| Indica II | 465 | 5.60% | 0.00% | 5.16% | 89.25% | NA |
| Indica III | 913 | 15.90% | 0.40% | 16.10% | 67.58% | NA |
| Indica Intermediate | 786 | 7.60% | 0.80% | 9.16% | 82.44% | NA |
| Temperate Japonica | 767 | 38.50% | 0.00% | 0.39% | 61.15% | NA |
| Tropical Japonica | 504 | 3.00% | 0.00% | 4.17% | 92.86% | NA |
| Japonica Intermediate | 241 | 5.40% | 0.00% | 1.24% | 93.36% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 23.96% | 72.92% | NA |
| Intermediate | 90 | 18.90% | 1.10% | 8.89% | 71.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0142999472 | A -> G | LOC_Os01g74230.1 | missense_variant ; p.Leu1177Pro; MODERATE | nonsynonymous_codon ; L1177P | Average:7.978; most accessible tissue: Callus, score: 15.971 | probably damaging  |
2.98 |
DELETERIOUS | 0.00 |
| vg0142999472 | A -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:7.978; most accessible tissue: Callus, score: 15.971 | N | N | N | N |