Search for Variation information by Variation ID:
Detailed information for vg0128724237:
| Variant ID: vg0128724237 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28724237 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCTGGAAGCAGATGCAACGTGGGAGCACGGTTTGTCTGCTGATGACGTGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAG[T/C]
TTAGCATGTCGCACGTCTGTCCTTCTTCATACAATGACTTCTTTGCAATGGTTGCGATGAAGCCTGGAATGTATCTAGCCGGGACTGGCGTGCTAACTCC
Reverse complement sequence
GGAGTTAGCACGCCAGTCCCGGCTAGATACATTCCAGGCTTCATCGCAACCATTGCAAAGAAGTCATTGTATGAAGAAGGACAGACGTGCGACATGCTAA[A/G]
CTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCACGTCATCAGCAGACAAACCGTGCTCCCACGTTGCATCTGCTTCCAGC
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 | 68.40% | 1.00% | 4.10% | 26.56% | NA |
| All Indica | 2759 | 58.70% | 1.20% | 2.61% | 37.51% | NA |
| All Japonica | 1512 | 88.80% | 0.00% | 0.93% | 10.25% | NA |
| Aus | 269 | 56.50% | 5.20% | 35.69% | 2.60% | NA |
| Indica I | 595 | 50.10% | 0.20% | 3.03% | 46.72% | NA |
| Indica II | 465 | 52.30% | 0.00% | 1.29% | 46.45% | NA |
| Indica III | 913 | 69.30% | 2.20% | 1.86% | 26.62% | NA |
| Indica Intermediate | 786 | 56.70% | 1.40% | 3.94% | 37.91% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 69.80% | 0.00% | 2.58% | 27.58% | NA |
| Japonica Intermediate | 241 | 95.00% | 0.00% | 0.41% | 4.56% | NA |
| VI/Aromatic | 96 | 50.00% | 0.00% | 9.38% | 40.62% | NA |
| Intermediate | 90 | 75.60% | 0.00% | 3.33% | 21.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128724237 | T -> DEL | LOC_Os01g49990.1 | N | frameshift_variant | Average:11.799; most accessible tissue: Callus, score: 22.262 | N | N | N | N |
| vg0128724237 | T -> C | LOC_Os01g49990.1 | missense_variant ; p.Phe44Leu; MODERATE | nonsynonymous_codon ; F44L | Average:11.799; most accessible tissue: Callus, score: 22.262 | benign  |
1.293 |
TOLERATED | 0.10 |