Search for Variation information by Variation ID:
Detailed information for vg0306598647:
| Variant ID: vg0306598647 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 6598647 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GATGTTAAGGCTTATATGTGTTAAATCTTTGAGAAAGATTCCTTTGATGGACTTACCATTGTAACAATTCAGAGGATATTGGAGAAAAAATTTAACAGGA[C/T]
GATGACTGTTCACGAACAGATTGTATTCAAGACTGCTTTTATAATCTTCGTTGTAACCAAATTCTTGGCTCCTCAATCTGTTAACAATCACATATCTATA
Reverse complement sequence
TATAGATATGTGATTGTTAACAGATTGAGGAGCCAAGAATTTGGTTACAACGAAGATTATAAAAGCAGTCTTGAATACAATCTGTTCGTGAACAGTCATC[G/A]
TCCTGTTAAATTTTTTCTCCAATATCCTCTGAATTGTTACAATGGTAAGTCCATCAAAGGAATCTTTCTCAAAGATTTAACACATATAAGCCTTAACATC
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 | 53.00% | 0.30% | 2.98% | 43.69% | NA |
| All Indica | 2759 | 29.10% | 0.50% | 4.35% | 66.11% | NA |
| All Japonica | 1512 | 98.30% | 0.00% | 0.73% | 0.99% | NA |
| Aus | 269 | 29.00% | 0.00% | 2.23% | 68.77% | NA |
| Indica I | 595 | 31.90% | 0.00% | 12.44% | 55.63% | NA |
| Indica II | 465 | 22.20% | 0.00% | 0.43% | 77.42% | NA |
| Indica III | 913 | 34.80% | 0.50% | 1.97% | 62.65% | NA |
| Indica Intermediate | 786 | 24.30% | 1.00% | 3.31% | 71.37% | NA |
| Temperate Japonica | 767 | 98.40% | 0.00% | 0.26% | 1.30% | NA |
| Tropical Japonica | 504 | 97.60% | 0.00% | 1.79% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 80.20% | 0.00% | 2.08% | 17.71% | NA |
| Intermediate | 90 | 71.10% | 0.00% | 2.22% | 26.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0306598647 | C -> T | LOC_Os03g12480.1 | missense_variant ; p.Thr78Met; MODERATE | nonsynonymous_codon ; T78M | Average:4.378; most accessible tissue: Minghui63 panicle, score: 7.125 | probably damaging  |
2.771 |
DELETERIOUS | 0.01 |
| vg0306598647 | C -> DEL | LOC_Os03g12480.1 | N | frameshift_variant | Average:4.378; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |