Search for Variation information by Variation ID:
Detailed information for vg0139513841:
| Variant ID: vg0139513841 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39513841 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGCCATCTTGCATGCATGTAGAGCTAAGAACGCCCTTTACAGCACACTCTTGCCAGGATGTTCAATTGAGGGGAATTTCTTCACTTCGTAAGAGCTCCCA[G/A]
GGTTTCTTTCCTCGATAACATCAAGCAGGCGTGGCAAATTGTCATATGAGGCTTTGTAAGTTCCAAATCTCATCTCTATTATTTTCTGTTTGGCCCTCCA
Reverse complement sequence
TGGAGGGCCAAACAGAAAATAATAGAGATGAGATTTGGAACTTACAAAGCCTCATATGACAATTTGCCACGCCTGCTTGATGTTATCGAGGAAAGAAACC[C/T]
TGGGAGCTCTTACGAAGTGAAGAAATTCCCCTCAATTGAACATCCTGGCAAGAGTGTGCTGTAAAGGGCGTTCTTAGCTCTACATGCATGCAAGATGGCA
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 | 25.30% | 0.60% | 2.64% | 71.43% | NA |
| All Indica | 2759 | 1.80% | 0.10% | 1.99% | 96.12% | NA |
| All Japonica | 1512 | 73.20% | 1.50% | 1.92% | 23.35% | NA |
| Aus | 269 | 0.40% | 0.00% | 5.20% | 94.42% | NA |
| Indica I | 595 | 3.50% | 0.30% | 1.34% | 94.79% | NA |
| Indica II | 465 | 0.60% | 0.00% | 0.86% | 98.49% | NA |
| Indica III | 913 | 0.70% | 0.00% | 1.10% | 98.25% | NA |
| Indica Intermediate | 786 | 2.50% | 0.00% | 4.20% | 93.26% | NA |
| Temperate Japonica | 767 | 94.30% | 2.90% | 0.13% | 2.74% | NA |
| Tropical Japonica | 504 | 52.80% | 0.00% | 4.56% | 42.66% | NA |
| Japonica Intermediate | 241 | 49.00% | 0.40% | 2.07% | 48.55% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 22.92% | 73.96% | NA |
| Intermediate | 90 | 41.10% | 2.20% | 5.56% | 51.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139513841 | G -> A | LOC_Os01g67990.1 | missense_variant ; p.Pro383Leu; MODERATE | nonsynonymous_codon ; P383L | Average:6.876; most accessible tissue: Callus, score: 26.099 | possibly damaging  |
1.861 |
DELETERIOUS | 0.04 |
| vg0139513841 | G -> DEL | LOC_Os01g67990.1 | N | frameshift_variant | Average:6.876; most accessible tissue: Callus, score: 26.099 | N | N | N | N |