Search for Variation information by Variation ID:
Detailed information for vg0910657564:
| Variant ID: vg0910657564 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 10657564 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGCTCCATACAAGCAAGCGCGACTTTGAGGTCGCCATGGTCGGTGATGGGGCCACCGGGTCCCGGCATCTTCATCTGAAGATAGGCGTAGTGGACCGCCG[A/C]
CATGAACTTCACCAACGCGGGCCTCCCCAGGACCGCGTTGTAGGGCAGACTGAGGTCCGCCACATCGAAGTCCACCCGCTCCGTGCGGAAGTTGGCGGAA
Reverse complement sequence
TTCCGCCAACTTCCGCACGGAGCGGGTGGACTTCGATGTGGCGGACCTCAGTCTGCCCTACAACGCGGTCCTGGGGAGGCCCGCGTTGGTGAAGTTCATG[T/G]
CGGCGGTCCACTACGCCTATCTTCAGATGAAGATGCCGGGACCCGGTGGCCCCATCACCGACCATGGCGACCTCAAAGTCGCGCTTGCTTGTATGGAGCA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 38.10% | 0.60% | 13.58% | 47.67% | NA |
| All Indica | 2759 | 29.20% | 0.20% | 20.30% | 50.27% | NA |
| All Japonica | 1512 | 54.60% | 1.60% | 1.06% | 42.79% | NA |
| Aus | 269 | 38.30% | 0.00% | 21.19% | 40.52% | NA |
| Indica I | 595 | 42.40% | 0.30% | 10.92% | 46.39% | NA |
| Indica II | 465 | 22.60% | 0.00% | 13.55% | 63.87% | NA |
| Indica III | 913 | 22.30% | 0.10% | 32.75% | 44.80% | NA |
| Indica Intermediate | 786 | 31.20% | 0.40% | 16.92% | 51.53% | NA |
| Temperate Japonica | 767 | 76.90% | 0.10% | 0.65% | 22.29% | NA |
| Tropical Japonica | 504 | 26.60% | 4.60% | 1.79% | 67.06% | NA |
| Japonica Intermediate | 241 | 41.90% | 0.00% | 0.83% | 57.26% | NA |
| VI/Aromatic | 96 | 32.30% | 0.00% | 4.17% | 63.54% | NA |
| Intermediate | 90 | 40.00% | 0.00% | 5.56% | 54.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0910657564 | A -> DEL | LOC_Os09g17420.1 | N | frameshift_variant | Average:10.434; most accessible tissue: Callus, score: 24.426 | N | N | N | N |
| vg0910657564 | A -> C | LOC_Os09g17420.1 | missense_variant ; p.Ser103Ala; MODERATE | nonsynonymous_codon ; S103A | Average:10.434; most accessible tissue: Callus, score: 24.426 | possibly damaging  |
-1.662 |
TOLERATED | 1.00 |