Search for Variation information by Variation ID:
Detailed information for vg0131446155:
| Variant ID: vg0131446155 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31446155 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GAGGGGTCCGTGCTGGCCTCGGGGATCGAGACGGGCTCGGGAGCCGGGGTCCACTCTGCCACAAAATCGGCGAGGGCCTGGCTCTTGATAGCGTGGCGTG[G/A]
TTCAAAGTGCAAATCGAACTCAGAAAGTTCGATTGCCCATTTCACCACCCGTCCTGTACCCTCTCGATTATGCAAGATTTGACCGAGGGGGTAAGACGTA
Reverse complement sequence
TACGTCTTACCCCCTCGGTCAAATCTTGCATAATCGAGAGGGTACAGGACGGGTGGTGAAATGGGCAATCGAACTTTCTGAGTTCGATTTGCACTTTGAA[C/T]
CACGCCACGCTATCAAGAGCCAGGCCCTCGCCGATTTTGTGGCAGAGTGGACCCCGGCTCCCGAGCCCGTCTCGATCCCCGAGGCCAGCACGGACCCCTC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 22.40% | 0.20% | 14.20% | 63.27% | NA |
| All Indica | 2759 | 3.10% | 0.00% | 8.19% | 88.69% | NA |
| All Japonica | 1512 | 59.60% | 0.40% | 23.21% | 16.80% | NA |
| Aus | 269 | 1.50% | 0.00% | 2.60% | 95.91% | NA |
| Indica I | 595 | 3.50% | 0.00% | 5.21% | 91.26% | NA |
| Indica II | 465 | 1.30% | 0.00% | 10.54% | 88.17% | NA |
| Indica III | 913 | 2.20% | 0.10% | 7.78% | 89.92% | NA |
| Indica Intermediate | 786 | 4.80% | 0.00% | 9.54% | 85.62% | NA |
| Temperate Japonica | 767 | 71.10% | 0.00% | 16.69% | 12.26% | NA |
| Tropical Japonica | 504 | 56.00% | 1.20% | 33.13% | 9.72% | NA |
| Japonica Intermediate | 241 | 30.70% | 0.00% | 23.24% | 46.06% | NA |
| VI/Aromatic | 96 | 27.10% | 0.00% | 68.75% | 4.17% | NA |
| Intermediate | 90 | 45.60% | 1.10% | 23.33% | 30.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131446155 | G -> A | LOC_Os01g54660.1 | missense_variant ; p.Pro1394Ser; MODERATE | nonsynonymous_codon ; P1394S | Average:12.796; most accessible tissue: Zhenshan97 flag leaf, score: 38.066 | benign  |
0.589 |
DELETERIOUS | 0.02 |
| vg0131446155 | G -> DEL | LOC_Os01g54660.1 | N | frameshift_variant | Average:12.796; most accessible tissue: Zhenshan97 flag leaf, score: 38.066 | N | N | N | N |