Search for Variation information by Variation ID:
Detailed information for vg0512022795:
| Variant ID: vg0512022795 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12022795 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGATGACAATGCATGAACAGTTACAACTCGACCATCATCGCTGGTGAGAGTTACTTTTTTGTTGGCACAGTCTATCACACCTTTATGTTTGGCTAACCAG[T/C]
CCATCCCTAGGATGACATCAAGGTCTTTGGATTCTAACAAGATAAGATTGGCCAGAAATGGTACTCCTTGAATTTCTATTCTGACAGAGGGGCTACGTTG
Reverse complement sequence
CAACGTAGCCCCTCTGTCAGAATAGAAATTCAAGGAGTACCATTTCTGGCCAATCTTATCTTGTTAGAATCCAAAGACCTTGATGTCATCCTAGGGATGG[A/G]
CTGGTTAGCCAAACATAAAGGTGTGATAGACTGTGCCAACAAAAAAGTAACTCTCACCAGCGATGATGGTCGAGTTGTAACTGTTCATGCATTGTCATCT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 87.30% | 0.30% | 4.27% | 8.15% | NA |
| All Indica | 2759 | 86.50% | 0.50% | 5.29% | 7.68% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.07% | 0.26% | NA |
| Aus | 269 | 21.60% | 0.00% | 17.47% | 60.97% | NA |
| Indica I | 595 | 91.90% | 0.00% | 3.03% | 5.04% | NA |
| Indica II | 465 | 98.30% | 0.00% | 0.65% | 1.08% | NA |
| Indica III | 913 | 79.20% | 0.00% | 9.97% | 10.84% | NA |
| Indica Intermediate | 786 | 83.80% | 1.90% | 4.33% | 9.92% | 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 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 90.00% | 0.00% | 5.56% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512022795 | T -> DEL | LOC_Os05g20480.1 | N | frameshift_variant | Average:26.185; most accessible tissue: Minghui63 flag leaf, score: 35.832 | N | N | N | N |
| vg0512022795 | T -> C | LOC_Os05g20480.1 | missense_variant ; p.Asp223Gly; MODERATE | nonsynonymous_codon ; D223G | Average:26.185; most accessible tissue: Minghui63 flag leaf, score: 35.832 | possibly damaging  |
1.867 |
DELETERIOUS | 0.00 |