Search for Variation information by Variation ID:
Detailed information for vg0610040562:
| Variant ID: vg0610040562 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 10040562 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.77, A: 0.23, others allele: 0.00, population size: 34. )
Flanking Sequence (100 bp) in Reference Genome:
TCTTACCTTTATTGATAAGTTCTTGAAAGGAATATGCAGCTCACATGGTGTCCGCTGAGTGATGTCATCAACGGGACAGGTCGATTCGTCCTGTGTTTGC[T/A]
TGGCGTCCATGCTCTGTGATCCTACCTGCCCCGTTGAGGCGCAGCTGCTACGGTTTCCTGACGGGCTCACCATTGCAGGAGGAATGGTCGGCTGGGGATC
Reverse complement sequence
GATCCCCAGCCGACCATTCCTCCTGCAATGGTGAGCCCGTCAGGAAACCGTAGCAGCTGCGCCTCAACGGGGCAGGTAGGATCACAGAGCATGGACGCCA[A/T]
GCAAACACAGGACGAATCGACCTGTCCCGTTGATGACATCACTCAGCGGACACCATGTGAGCTGCATATTCCTTTCAAGAACTTATCAATAAAGGTAAGA
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 2.70% | 0.20% | 18.98% | 78.12% | NA |
| All Indica | 2759 | 0.60% | 0.10% | 24.21% | 75.14% | NA |
| All Japonica | 1512 | 7.30% | 0.40% | 8.33% | 83.93% | NA |
| Aus | 269 | 0.00% | 0.00% | 28.25% | 71.75% | NA |
| Indica I | 595 | 0.30% | 0.00% | 7.90% | 91.76% | NA |
| Indica II | 465 | 0.00% | 0.00% | 7.53% | 92.47% | NA |
| Indica III | 913 | 0.50% | 0.20% | 46.00% | 53.23% | NA |
| Indica Intermediate | 786 | 1.10% | 0.00% | 21.12% | 77.74% | NA |
| Temperate Japonica | 767 | 14.10% | 0.80% | 10.95% | 74.19% | NA |
| Tropical Japonica | 504 | 0.00% | 0.00% | 5.95% | 94.05% | NA |
| Japonica Intermediate | 241 | 1.20% | 0.00% | 4.98% | 93.78% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 12.50% | 86.46% | NA |
| Intermediate | 90 | 1.10% | 0.00% | 16.67% | 82.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0610040562 | T -> A | LOC_Os06g17330.1 | missense_variant ; p.Lys443Met; MODERATE | nonsynonymous_codon ; K443M | Average:11.807; most accessible tissue: Minghui63 panicle, score: 20.733 | benign  |
-0.449 |
TOLERATED | 1.00 |
| vg0610040562 | T -> DEL | LOC_Os06g17330.1 | N | frameshift_variant | Average:11.807; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |