Search for Variation information by Variation ID:
Detailed information for vg0131448296:
| Variant ID: vg0131448296 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31448296 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATCTTCATCTGTAGGTAGGCGTAGTGGACCGCCGCCATGAACTTCACCAACGCGGGCCTCCCCAGGACCGCGTTGTAGGGCAGACTGAGGTCCGCCACAT[C/T]
GAAGTTCACCCGCTCCGTGCGGAAGTTGGCGGATCCACCGAAGGTGACCGGTAGGTCGATGTGACCTAACGGCCACGTGTGCCCCGGCGTCACACCGATA
Reverse complement sequence
TATCGGTGTGACGCCGGGGCACACGTGGCCGTTAGGTCACATCGACCTACCGGTCACCTTCGGTGGATCCGCCAACTTCCGCACGGAGCGGGTGAACTTC[G/A]
ATGTGGCGGACCTCAGTCTGCCCTACAACGCGGTCCTGGGGAGGCCCGCGTTGGTGAAGTTCATGGCGGCGGTCCACTACGCCTACCTACAGATGAAGAT
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 | 27.60% | 4.20% | 6.75% | 61.45% | NA |
| All Indica | 2759 | 3.00% | 0.00% | 10.69% | 86.26% | NA |
| All Japonica | 1512 | 70.60% | 12.70% | 0.60% | 16.14% | NA |
| Aus | 269 | 1.50% | 0.00% | 4.09% | 94.42% | NA |
| Indica I | 595 | 4.00% | 0.00% | 9.41% | 86.55% | NA |
| Indica II | 465 | 1.30% | 0.00% | 9.68% | 89.03% | NA |
| Indica III | 913 | 1.30% | 0.10% | 11.50% | 87.08% | NA |
| Indica Intermediate | 786 | 5.20% | 0.00% | 11.32% | 83.46% | NA |
| Temperate Japonica | 767 | 87.50% | 0.30% | 0.13% | 12.13% | NA |
| Tropical Japonica | 504 | 54.60% | 36.10% | 1.19% | 8.13% | NA |
| Japonica Intermediate | 241 | 50.20% | 3.30% | 0.83% | 45.64% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 0.00% | 3.12% | NA |
| Intermediate | 90 | 62.20% | 7.80% | 4.44% | 25.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131448296 | C -> T | LOC_Os01g54660.1 | missense_variant ; p.Asp693Asn; MODERATE | nonsynonymous_codon ; D693N | Average:36.082; most accessible tissue: Zhenshan97 root, score: 65.566 | benign  |
0.601 |
DELETERIOUS | 0.00 |
| vg0131448296 | C -> DEL | LOC_Os01g54660.1 | N | frameshift_variant | Average:36.082; most accessible tissue: Zhenshan97 root, score: 65.566 | N | N | N | N |