Search for Variation information by Variation ID:
Detailed information for vg0512023267:
| Variant ID: vg0512023267 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12023267 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGGGGCTTCGGACACTTGTCAGCATAATGTCCTGGATCTCCACAGTTGAAACACACCACGGGCTTGTTGCCTTGCTCCCTCTTGGCAGGTTGTTGCTGTG[C/T]
TGGAGCTGCAACAGGACGTGGAGCTTGATTACGGATGTTGTTGCCAGCATTGTTGTTGAAGAACTGACGCTGCGGACGAACAACAGACGAAGAACCTCCC
Reverse complement sequence
GGGAGGTTCTTCGTCTGTTGTTCGTCCGCAGCGTCAGTTCTTCAACAACAATGCTGGCAACAACATCCGTAATCAAGCTCCACGTCCTGTTGCAGCTCCA[G/A]
CACAGCAACAACCTGCCAAGAGGGAGCAAGGCAACAAGCCCGTGGTGTGTTTCAACTGTGGAGATCCAGGACATTATGCTGACAAGTGTCCGAAGCCCCG
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 | 87.80% | 4.00% | 6.71% | 1.48% | NA |
| All Indica | 2759 | 87.00% | 4.30% | 7.72% | 0.94% | NA |
| All Japonica | 1512 | 99.50% | 0.20% | 0.26% | 0.00% | NA |
| Aus | 269 | 27.10% | 23.40% | 33.83% | 15.61% | NA |
| Indica I | 595 | 92.30% | 0.70% | 7.06% | 0.00% | NA |
| Indica II | 465 | 98.30% | 0.60% | 1.08% | 0.00% | NA |
| Indica III | 913 | 78.40% | 10.50% | 9.09% | 1.97% | NA |
| Indica Intermediate | 786 | 86.30% | 2.20% | 10.56% | 1.02% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.80% | 0.40% | 0.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 1.00% | 4.17% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 1.10% | 5.56% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512023267 | C -> T | LOC_Os05g20480.1 | missense_variant ; p.Ala66Thr; MODERATE | nonsynonymous_codon ; A66T | Average:27.554; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 | benign  |
-0.105 |
TOLERATED | 0.78 |
| vg0512023267 | C -> DEL | LOC_Os05g20480.1 | N | frameshift_variant | Average:27.554; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 | N | N | N | N |