Search for Variation information by Variation ID:
Detailed information for vg0625554606:
| Variant ID: vg0625554606 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 25554606 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGCATCTCTTTCTCCGAATCTGGGACAAAGCTCTCATGATCTCCGTGTGCCCTTGTTCTTCGCCAGTACACCGTACTGACAGGCACGTTATCCCGCACAA[C/T]
CCAACCGCTGTGACGTACATAGTTCTTGGTGGCTTCGGCTGGGGCACTAGGACGTCCATCTTCTTCCACTTCCGTTATGATGTGCCGACCCTCAAGCTTC
Reverse complement sequence
GAAGCTTGAGGGTCGGCACATCATAACGGAAGTGGAAGAAGATGGACGTCCTAGTGCCCCAGCCGAAGCCACCAAGAACTATGTACGTCACAGCGGTTGG[G/A]
TTGTGCGGGATAACGTGCCTGTCAGTACGGTGTACTGGCGAAGAACAAGGGCACACGGAGATCATGAGAGCTTTGTCCCAGATTCGGAGAAAGAGATGCT
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 | 65.00% | 1.60% | 9.18% | 24.23% | NA |
| All Indica | 2759 | 75.20% | 2.30% | 10.40% | 12.03% | NA |
| All Japonica | 1512 | 52.80% | 0.00% | 2.84% | 44.38% | NA |
| Aus | 269 | 34.60% | 3.70% | 28.62% | 33.09% | NA |
| Indica I | 595 | 60.00% | 0.50% | 12.94% | 26.55% | NA |
| Indica II | 465 | 75.70% | 1.90% | 13.98% | 8.39% | NA |
| Indica III | 913 | 88.80% | 2.50% | 6.02% | 2.63% | NA |
| Indica Intermediate | 786 | 70.70% | 3.70% | 11.45% | 14.12% | NA |
| Temperate Japonica | 767 | 65.30% | 0.00% | 0.91% | 33.77% | NA |
| Tropical Japonica | 504 | 34.90% | 0.00% | 4.96% | 60.12% | NA |
| Japonica Intermediate | 241 | 50.20% | 0.00% | 4.56% | 45.23% | NA |
| VI/Aromatic | 96 | 50.00% | 0.00% | 16.67% | 33.33% | NA |
| Intermediate | 90 | 62.20% | 2.20% | 12.22% | 23.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0625554606 | C -> T | LOC_Os06g42500.1 | missense_variant ; p.Val119Ile; MODERATE | nonsynonymous_codon ; V119I | Average:16.05; most accessible tissue: Minghui63 young leaf, score: 24.836 | benign  |
0.494 |
DELETERIOUS | 0.00 |
| vg0625554606 | C -> DEL | LOC_Os06g42500.1 | N | frameshift_variant | Average:16.05; most accessible tissue: Minghui63 young leaf, score: 24.836 | N | N | N | N |