Search for Variation information by Variation ID:
Detailed information for vg1212666160:
| Variant ID: vg1212666160 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666160 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGCTCCAGAAGATGTGCGTACTGACGAGGAAAGGCAGGAGAAGTTCTTGGAAGGCTTAAAGGATGAACTGTCAGTTACGTTAATCTCCCATGACTATGTT[G/A]
ATTTTCAGCAGCTGGTTGACAAAGCAATTCGCCTTGAAGACAAGAAGAACAGGATGGATAACCGTAAAAGGAAAATGACTGTTTTCCAGGAGGCACAAGG
Reverse complement sequence
CCTTGTGCCTCCTGGAAAACAGTCATTTTCCTTTTACGGTTATCCATCCTGTTCTTCTTGTCTTCAAGGCGAATTGCTTTGTCAACCAGCTGCTGAAAAT[C/T]
AACATAGTCATGGGAGATTAACGTAACTGACAGTTCATCCTTTAAGCCTTCCAAGAACTTCTCCTGCCTTTCCTCGTCAGTACGCACATCTTCTGGAGCA
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 | 36.10% | 0.70% | 19.15% | 44.14% | NA |
| All Indica | 2759 | 32.30% | 1.10% | 22.47% | 44.07% | NA |
| All Japonica | 1512 | 44.60% | 0.00% | 3.64% | 51.79% | NA |
| Aus | 269 | 29.70% | 0.00% | 59.48% | 10.78% | NA |
| Indica I | 595 | 14.80% | 0.00% | 13.78% | 71.43% | NA |
| Indica II | 465 | 40.20% | 0.00% | 16.56% | 43.23% | NA |
| Indica III | 913 | 38.80% | 2.30% | 30.23% | 28.70% | NA |
| Indica Intermediate | 786 | 33.50% | 1.30% | 23.54% | 41.73% | NA |
| Temperate Japonica | 767 | 77.80% | 0.00% | 2.09% | 20.08% | NA |
| Tropical Japonica | 504 | 3.20% | 0.00% | 5.36% | 91.47% | NA |
| Japonica Intermediate | 241 | 25.30% | 0.00% | 4.98% | 69.71% | NA |
| VI/Aromatic | 96 | 19.80% | 0.00% | 54.17% | 26.04% | NA |
| Intermediate | 90 | 43.30% | 0.00% | 20.00% | 36.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666160 | G -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1212666160 | G -> A | LOC_Os12g22430.1 | missense_variant ; p.Asp209Asn; MODERATE | nonsynonymous_codon ; D209N | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | probably damaging  |
2.055 |
DELETERIOUS | 0.01 |