Search for Variation information by Variation ID:
Detailed information for vg0512020095:
| Variant ID: vg0512020095 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12020095 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CAATTGTGACACATGGAACACATTATGGACTCCTGCCAAAGATTGAGGTAATTCTAACTGATAAGCAACCTCTCCTCTTCTACTGACAATCTTATAAGGT[C/T]
CCACAAAACGCGGTGCCAATTTTCCCTTGGTGTGAAAACGATGAACTCCTCGAAGAGGCGTGACACGAAGATACACATAGTCTCCTTCTTCAAAACTCAA
Reverse complement sequence
TTGAGTTTTGAAGAAGGAGACTATGTGTATCTTCGTGTCACGCCTCTTCGAGGAGTTCATCGTTTTCACACCAAGGGAAAATTGGCACCGCGTTTTGTGG[G/A]
ACCTTATAAGATTGTCAGTAGAAGAGGAGAGGTTGCTTATCAGTTAGAATTACCTCAATCTTTGGCAGGAGTCCATAATGTGTTCCATGTGTCACAATTG
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 | 88.00% | 0.10% | 3.45% | 8.46% | NA |
| All Indica | 2759 | 87.50% | 0.10% | 3.91% | 8.48% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Aus | 269 | 23.80% | 0.00% | 18.22% | 57.99% | NA |
| Indica I | 595 | 92.10% | 0.00% | 2.02% | 5.88% | NA |
| Indica II | 465 | 97.80% | 0.20% | 0.65% | 1.29% | NA |
| Indica III | 913 | 80.30% | 0.00% | 8.00% | 11.72% | NA |
| Indica Intermediate | 786 | 86.10% | 0.40% | 2.54% | 10.94% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 2.08% | 1.04% | NA |
| Intermediate | 90 | 90.00% | 0.00% | 4.44% | 5.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512020095 | C -> T | LOC_Os05g20480.1 | missense_variant ; p.Gly1123Glu; MODERATE | nonsynonymous_codon ; G1123E | Average:6.18; most accessible tissue: Minghui63 young leaf, score: 9.976 | benign  |
1.421 |
DELETERIOUS | 0.00 |
| vg0512020095 | C -> DEL | LOC_Os05g20480.1 | N | frameshift_variant | Average:6.18; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |