Search for Variation information by Variation ID:
Detailed information for vg0610040638:
| Variant ID: vg0610040638 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 10040638 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CAGGTCGATTCGTCCTGTGTTTGCTTGGCGTCCATGCTCTGTGATCCTACCTGCCCCGTTGAGGCGCAGCTGCTACGGTTTCCTGACGGGCTCACCATTG[C/T]
AGGAGGAATGGTCGGCTGGGGATCATGGGACCGATGTGCGGCCATGCGTTCATCAACCTTCCTTGCCACCTCCTCTTTCATGTTGAGTTCGTAGCTCGAT
Reverse complement sequence
ATCGAGCTACGAACTCAACATGAAAGAGGAGGTGGCAAGGAAGGTTGATGAACGCATGGCCGCACATCGGTCCCATGATCCCCAGCCGACCATTCCTCCT[G/A]
CAATGGTGAGCCCGTCAGGAAACCGTAGCAGCTGCGCCTCAACGGGGCAGGTAGGATCACAGAGCATGGACGCCAAGCAAACACAGGACGAATCGACCTG
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 | 11.90% | 0.30% | 15.87% | 71.90% | NA |
| All Indica | 2759 | 5.00% | 0.00% | 21.96% | 73.03% | NA |
| All Japonica | 1512 | 27.20% | 1.10% | 3.70% | 67.99% | NA |
| Aus | 269 | 0.00% | 0.00% | 23.05% | 76.95% | NA |
| Indica I | 595 | 3.50% | 0.00% | 6.39% | 90.08% | NA |
| Indica II | 465 | 0.60% | 0.00% | 7.31% | 92.04% | NA |
| Indica III | 913 | 6.60% | 0.00% | 42.61% | 50.82% | NA |
| Indica Intermediate | 786 | 6.90% | 0.00% | 18.45% | 74.68% | NA |
| Temperate Japonica | 767 | 50.70% | 2.10% | 3.39% | 43.81% | NA |
| Tropical Japonica | 504 | 1.00% | 0.00% | 4.37% | 94.64% | NA |
| Japonica Intermediate | 241 | 7.50% | 0.00% | 3.32% | 89.21% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 11.46% | 83.33% | NA |
| Intermediate | 90 | 7.80% | 0.00% | 16.67% | 75.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0610040638 | C -> T | LOC_Os06g17330.1 | missense_variant ; p.Ala418Thr; MODERATE | nonsynonymous_codon ; A418T | Average:11.886; most accessible tissue: Minghui63 panicle, score: 20.733 | benign  |
0.381 |
DELETERIOUS | 0.04 |
| vg0610040638 | C -> DEL | LOC_Os06g17330.1 | N | frameshift_variant | Average:11.886; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |