Search for Variation information by Variation ID:
Detailed information for vg0204160066:
| Variant ID: vg0204160066 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 4160066 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCAGGCGCATCGGGTCACGGTGGTTACGTCTTATCCCCTCGGCCAAATCTTGTATAACCGAGAGGGTACTGGACGGGTGGTGAAATGGGCAATCGAACTC[T/C]
CTGAATTCGATTTGCGCTTTGAACCAAGCCACGCGATCAAGAGCCAGGCCCTCGCCGACTTTGTGGTGGAGTGGACCCCAGCTCCCGAGCTCGTCTCTGT
Reverse complement sequence
ACAGAGACGAGCTCGGGAGCTGGGGTCCACTCCACCACAAAGTCGGCGAGGGCCTGGCTCTTGATCGCGTGGCTTGGTTCAAAGCGCAAATCGAATTCAG[A/G]
GAGTTCGATTGCCCATTTCACCACCCGTCCAGTACCCTCTCGGTTATACAAGATTTGGCCGAGGGGATAAGACGTAACCACCGTGACCCGATGCGCCTGG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 80.60% | 0.20% | 3.98% | 15.19% | NA |
| All Indica | 2759 | 76.20% | 0.00% | 3.41% | 20.44% | NA |
| All Japonica | 1512 | 91.60% | 0.60% | 5.56% | 2.25% | NA |
| Aus | 269 | 54.30% | 0.00% | 2.60% | 43.12% | NA |
| Indica I | 595 | 98.20% | 0.00% | 0.17% | 1.68% | NA |
| Indica II | 465 | 79.10% | 0.00% | 2.58% | 18.28% | NA |
| Indica III | 913 | 61.30% | 0.00% | 5.37% | 33.30% | NA |
| Indica Intermediate | 786 | 74.90% | 0.00% | 4.07% | 20.99% | NA |
| Temperate Japonica | 767 | 88.70% | 0.00% | 7.30% | 4.04% | NA |
| Tropical Japonica | 504 | 94.40% | 1.60% | 3.37% | 0.60% | NA |
| Japonica Intermediate | 241 | 95.00% | 0.40% | 4.56% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 0.00% | 3.33% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0204160066 | T -> DEL | LOC_Os02g07950.1 | N | frameshift_variant | Average:49.383; most accessible tissue: Zhenshan97 panicle, score: 72.468 | N | N | N | N |
| vg0204160066 | T -> C | LOC_Os02g07950.1 | missense_variant ; p.Ser176Pro; MODERATE | nonsynonymous_codon ; S176P | Average:49.383; most accessible tissue: Zhenshan97 panicle, score: 72.468 | probably damaging  |
2.04 |
DELETERIOUS | 0.00 |