Search for Variation information by Variation ID:
Detailed information for vg1002959463:
| Variant ID: vg1002959463 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 2959463 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTGGAAGTAGTCGTACAGGAACGCCGACGTGCACTCCGCTGGCGACGTGGAGGAGTACATCCTCTTGCCGGCGACGGCCACGAAGGTGTTAGCCTTATCG[A/C]
CGCCGTTGTCCGTTGTTGACGACAGCGGCACGATCTTGGACGGCTCCTGCCCGGGGCACGGCGTGCTGCTCGCCGCGCTGTGCAGCTGCGCGAAGCAGTC
Reverse complement sequence
GACTGCTTCGCGCAGCTGCACAGCGCGGCGAGCAGCACGCCGTGCCCCGGGCAGGAGCCGTCCAAGATCGTGCCGCTGTCGTCAACAACGGACAACGGCG[T/G]
CGATAAGGCTAACACCTTCGTGGCCGTCGCCGGCAAGAGGATGTACTCCTCCACGTCGCCAGCGGAGTGCACGTCGGCGTTCCTGTACGACTACTTCCAC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 26.70% | 17.00% | 25.16% | 31.13% | NA |
| All Indica | 2759 | 18.70% | 1.30% | 38.02% | 41.97% | NA |
| All Japonica | 1512 | 39.70% | 47.80% | 3.97% | 8.53% | NA |
| Aus | 269 | 28.30% | 5.20% | 7.81% | 58.74% | NA |
| Indica I | 595 | 7.60% | 1.20% | 43.70% | 47.56% | NA |
| Indica II | 465 | 13.50% | 2.20% | 34.41% | 49.89% | NA |
| Indica III | 913 | 30.60% | 0.50% | 37.46% | 31.43% | NA |
| Indica Intermediate | 786 | 16.50% | 1.70% | 36.51% | 45.29% | NA |
| Temperate Japonica | 767 | 11.10% | 78.70% | 3.39% | 6.78% | NA |
| Tropical Japonica | 504 | 83.90% | 6.90% | 2.58% | 6.55% | NA |
| Japonica Intermediate | 241 | 38.20% | 34.90% | 8.71% | 18.26% | NA |
| VI/Aromatic | 96 | 49.00% | 10.40% | 36.46% | 4.17% | NA |
| Intermediate | 90 | 25.60% | 23.30% | 26.67% | 24.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1002959463 | A -> C | LOC_Os10g05860.1 | missense_variant ; p.Val131Gly; MODERATE | nonsynonymous_codon ; V131G | Average:15.645; most accessible tissue: Zhenshan97 flower, score: 24.143 | benign  |
-0.625 |
TOLERATED | 0.42 |
| vg1002959463 | A -> DEL | LOC_Os10g05860.1 | N | frameshift_variant | Average:15.645; most accessible tissue: Zhenshan97 flower, score: 24.143 | N | N | N | N |