Search for Variation information by Variation ID:
Detailed information for vg0512023378:
| Variant ID: vg0512023378 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12023378 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACAGGACGTGGAGCTTGATTACGGATGTTGTTGCCAGCATTGTTGTTGAAGAACTGACGCTGCGGACGAACAACAGACGAAGAACCTCCCTGTGGCATGG[G/A]
CTGGGGTCCTAAAGTAAGACGCGGCTTCTGATTATTTCCCTGTTGTGTCTTGAATTGAGCAATCCGACGTTTCTTCTGCTCCATGCGATTGTACTTGTCC
Reverse complement sequence
GGACAAGTACAATCGCATGGAGCAGAAGAAACGTCGGATTGCTCAATTCAAGACACAACAGGGAAATAATCAGAAGCCGCGTCTTACTTTAGGACCCCAG[C/T]
CCATGCCACAGGGAGGTTCTTCGTCTGTTGTTCGTCCGCAGCGTCAGTTCTTCAACAACAATGCTGGCAACAACATCCGTAATCAAGCTCCACGTCCTGT
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 | 87.30% | 0.00% | 4.25% | 8.46% | NA |
| All Indica | 2759 | 86.40% | 0.00% | 4.93% | 8.63% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.07% | 0.26% | NA |
| Aus | 269 | 22.70% | 0.00% | 21.56% | 55.76% | NA |
| Indica I | 595 | 92.30% | 0.00% | 2.02% | 5.71% | NA |
| Indica II | 465 | 98.30% | 0.00% | 0.43% | 1.29% | NA |
| Indica III | 913 | 76.70% | 0.00% | 10.84% | 12.49% | NA |
| Indica Intermediate | 786 | 86.30% | 0.10% | 2.93% | 10.69% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.20% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 88.90% | 0.00% | 3.33% | 7.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512023378 | G -> DEL | LOC_Os05g20480.1 | N | frameshift_variant | Average:26.007; most accessible tissue: Zhenshan97 flag leaf, score: 41.874 | N | N | N | N |
| vg0512023378 | G -> A | LOC_Os05g20480.1 | missense_variant ; p.Pro29Ser; MODERATE | nonsynonymous_codon ; P29S | Average:26.007; most accessible tissue: Zhenshan97 flag leaf, score: 41.874 | benign  |
-0.21 |
TOLERATED | 1.00 |