Search for Variation information by Variation ID:
Detailed information for vg0420967437:
| Variant ID: vg0420967437 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20967437 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 122. )
Flanking Sequence (100 bp) in Reference Genome:
TGCAATCACCGGCACCACCTTTGAATTTTTTTTCTATATGGCGGCTTGGGAGGACAGGGCGGGCAGCAGCAGGCGAAGGGGCTGGGGCGCGTGAAGAACA[C/A]
GTACGCCTCGGTGGCCGAGTACCTCGCTGTGTTCGAGCCGCTGCTGTTCGAGGAGGTGAAGGCGCAGATCGTCCAGGGGCGCAGCGACGAGGAGGAAGGT
Reverse complement sequence
ACCTTCCTCCTCGTCGCTGCGCCCCTGGACGATCTGCGCCTTCACCTCCTCGAACAGCAGCGGCTCGAACACAGCGAGGTACTCGGCCACCGAGGCGTAC[G/T]
TGTTCTTCACGCGCCCCAGCCCCTTCGCCTGCTGCTGCCCGCCCTGTCCTCCCAAGCCGCCATATAGAAAAAAAATTCAAAGGTGGTGCCGGTGATTGCA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.70% | 29.90% | 8.78% | 4.61% | NA |
| All Indica | 2759 | 39.10% | 50.20% | 7.79% | 2.86% | NA |
| All Japonica | 1512 | 91.50% | 0.30% | 1.12% | 7.14% | NA |
| Aus | 269 | 37.20% | 1.50% | 60.97% | 0.37% | NA |
| Indica I | 595 | 77.00% | 20.50% | 1.68% | 0.84% | NA |
| Indica II | 465 | 14.00% | 66.50% | 9.68% | 9.89% | NA |
| Indica III | 913 | 35.90% | 55.10% | 8.43% | 0.55% | NA |
| Indica Intermediate | 786 | 29.10% | 57.40% | 10.56% | 2.93% | NA |
| Temperate Japonica | 767 | 99.70% | 0.10% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 78.40% | 0.60% | 2.98% | 18.06% | NA |
| Japonica Intermediate | 241 | 92.50% | 0.00% | 0.41% | 7.05% | NA |
| VI/Aromatic | 96 | 59.40% | 3.10% | 10.42% | 27.08% | NA |
| Intermediate | 90 | 67.80% | 17.80% | 10.00% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420967437 | C -> DEL | LOC_Os04g34670.1 | N | frameshift_variant | Average:44.296; most accessible tissue: Zhenshan97 panicle, score: 73.605 | N | N | N | N |
| vg0420967437 | C -> A | LOC_Os04g34670.1 | missense_variant ; p.Thr36Lys; MODERATE | nonsynonymous_codon ; T36K | Average:44.296; most accessible tissue: Zhenshan97 panicle, score: 73.605 | possibly damaging  |
1.538 |
TOLERATED | 0.13 |