Search for Variation information by Variation ID:
Detailed information for vg0125111953:
| Variant ID: vg0125111953 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 25111953 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACATTCCAGGCTTCATCGCAACCATTGCAAGGAAGTCATTGTATGAAGAAGGGCAGACGTGCGGCGTGCTAAACTGACACGTGGTGGACAAGAATGACCG[G/T]
TCTGTGACTGGTCTGACGCCGGTCACGTCATCGGCAGACAACCGAGCTCCCACGTTGCATCTGCTTCCGGCGGAGTGGAGGTAGATATGACCCATCCCAT
Reverse complement sequence
ATGGGATGGGTCATATCTACCTCCACTCCGCCGGAAGCAGATGCAACGTGGGAGCTCGGTTGTCTGCCGATGACGTGACCGGCGTCAGACCAGTCACAGA[C/A]
CGGTCATTCTTGTCCACCACGTGTCAGTTTAGCACGCCGCACGTCTGCCCTTCTTCATACAATGACTTCCTTGCAATGGTTGCGATGAAGCCTGGAATGT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 10.30% | 0.20% | 20.17% | 69.26% | NA |
| All Indica | 2759 | 1.30% | 0.00% | 13.01% | 85.61% | NA |
| All Japonica | 1512 | 24.20% | 0.50% | 34.66% | 40.67% | NA |
| Aus | 269 | 1.10% | 0.40% | 14.13% | 84.39% | NA |
| Indica I | 595 | 0.70% | 0.00% | 6.89% | 92.44% | NA |
| Indica II | 465 | 1.90% | 0.00% | 12.90% | 85.16% | NA |
| Indica III | 913 | 0.90% | 0.00% | 17.74% | 81.38% | NA |
| Indica Intermediate | 786 | 2.00% | 0.10% | 12.21% | 85.62% | NA |
| Temperate Japonica | 767 | 29.70% | 0.10% | 53.32% | 16.82% | NA |
| Tropical Japonica | 504 | 20.40% | 0.60% | 11.71% | 67.26% | NA |
| Japonica Intermediate | 241 | 14.50% | 1.20% | 23.24% | 61.00% | NA |
| VI/Aromatic | 96 | 67.70% | 0.00% | 11.46% | 20.83% | NA |
| Intermediate | 90 | 20.00% | 2.20% | 23.33% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0125111953 | G -> T | LOC_Os01g43830.1 | missense_variant ; p.Asp32Glu; MODERATE | nonsynonymous_codon ; D32E | Average:8.92; most accessible tissue: Zhenshan97 panicle, score: 16.188 | benign  |
1.487 |
DELETERIOUS | 0.02 |
| vg0125111953 | G -> DEL | LOC_Os01g43830.1 | N | frameshift_variant | Average:8.92; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |