Search for Variation information by Variation ID:
Detailed information for vg0139512433:
| Variant ID: vg0139512433 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39512433 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGGCGAGCTCCATCTGCTGCTGATCCTGATAGTCCTGCCTCCGCCGCACTTGGTTTCTCCTTGTCTTTAGGACAATGCTTGTAGGTGTGCCCATGTTCAT[T/C]
GTATTTGCTGCAACGCTTCACCCTGCCAGCCTCCGACTCGTCCATATTGTTGCGGATGCGACGAGTCCTCCTCCTTCCAGCCTTGCCTCGGAGCTTCGAT
Reverse complement sequence
ATCGAAGCTCCGAGGCAAGGCTGGAAGGAGGAGGACTCGTCGCATCCGCAACAATATGGACGAGTCGGAGGCTGGCAGGGTGAAGCGTTGCAGCAAATAC[A/G]
ATGAACATGGGCACACCTACAAGCATTGTCCTAAAGACAAGGAGAAACCAAGTGCGGCGGAGGCAGGACTATCAGGATCAGCAGCAGATGGAGCTCGCCC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 26.20% | 1.20% | 2.35% | 70.21% | NA |
| All Indica | 2759 | 2.50% | 0.80% | 3.19% | 93.55% | NA |
| All Japonica | 1512 | 74.70% | 0.30% | 0.13% | 24.87% | NA |
| Aus | 269 | 0.40% | 2.20% | 6.32% | 91.08% | NA |
| Indica I | 595 | 4.00% | 0.20% | 3.19% | 92.61% | NA |
| Indica II | 465 | 2.60% | 0.00% | 1.29% | 96.13% | NA |
| Indica III | 913 | 0.70% | 1.50% | 2.30% | 95.51% | NA |
| Indica Intermediate | 786 | 3.40% | 0.80% | 5.34% | 90.46% | NA |
| Temperate Japonica | 767 | 97.30% | 0.00% | 0.00% | 2.74% | NA |
| Tropical Japonica | 504 | 53.00% | 0.00% | 0.40% | 46.63% | NA |
| Japonica Intermediate | 241 | 48.50% | 1.70% | 0.00% | 49.79% | NA |
| VI/Aromatic | 96 | 2.10% | 24.00% | 4.17% | 69.79% | NA |
| Intermediate | 90 | 41.10% | 4.40% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0139512433 | T -> DEL | LOC_Os01g67990.1 | N | frameshift_variant | Average:7.02; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg0139512433 | T -> C | LOC_Os01g67990.1 | missense_variant ; p.Asn821Asp; MODERATE | nonsynonymous_codon | Average:7.02; most accessible tissue: Zhenshan97 root, score: 16.934 | benign  |
-0.407 |
TOLERATED | 1.00 |