Search for Variation information by Variation ID:
Detailed information for vg0614962488:
| Variant ID: vg0614962488 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 14962488 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AATAACAACTTATTTACTTACAGTGAACTGGAGCAACCAAGCCTTGCTAGGCCCGACTGTAGAGTACGGAGGAAGGGTGGTGGTCGGTCCTAGGTGTGGA[A/T]
GGCGCATCACCTGCTCGAAGCGCGCAGTGATATCCTCCTTCCACCCAAAAACACCGTCGACGGGACCAACTGGTGCTCCCGCCAGCGGTAGCCCGAGCAG
Reverse complement sequence
CTGCTCGGGCTACCGCTGGCGGGAGCACCAGTTGGTCCCGTCGACGGTGTTTTTGGGTGGAAGGAGGATATCACTGCGCGCTTCGAGCAGGTGATGCGCC[T/A]
TCCACACCTAGGACCGACCACCACCCTTCCTCCGTACTCTACAGTCGGGCCTAGCAAGGCTTGGTTGCTCCAGTTCACTGTAAGTAAATAAGTTGTTATT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.80% | 0.10% | 3.58% | 60.52% | NA |
| All Indica | 2759 | 4.60% | 0.10% | 4.24% | 91.05% | NA |
| All Japonica | 1512 | 82.80% | 0.10% | 1.79% | 15.28% | NA |
| Aus | 269 | 73.60% | 0.00% | 2.23% | 24.16% | NA |
| Indica I | 595 | 5.20% | 0.00% | 1.51% | 93.28% | NA |
| Indica II | 465 | 2.20% | 0.00% | 1.08% | 96.77% | NA |
| Indica III | 913 | 2.20% | 0.00% | 8.00% | 89.81% | NA |
| Indica Intermediate | 786 | 8.40% | 0.40% | 3.82% | 87.40% | NA |
| Temperate Japonica | 767 | 96.30% | 0.30% | 0.39% | 3.00% | NA |
| Tropical Japonica | 504 | 59.70% | 0.00% | 3.77% | 36.51% | NA |
| Japonica Intermediate | 241 | 88.00% | 0.00% | 2.07% | 9.96% | NA |
| VI/Aromatic | 96 | 76.00% | 0.00% | 14.58% | 9.38% | NA |
| Intermediate | 90 | 46.70% | 0.00% | 5.56% | 47.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0614962488 | A -> T | LOC_Os06g25580.1 | missense_variant ; p.Leu984His; MODERATE | nonsynonymous_codon ; L984H | Average:4.786; most accessible tissue: Minghui63 panicle, score: 7.125 | probably damaging  |
3.24 |
DELETERIOUS | 0.00 |
| vg0614962488 | A -> DEL | LOC_Os06g25580.1 | N | frameshift_variant | Average:4.786; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |