Search for Variation information by Variation ID:
Detailed information for vg1212666112:
| Variant ID: vg1212666112 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666112 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCATACCGTGGCAGAGTATCTTCATGAGTTCAATCGTTTGGCACGTTATGCTCCAGAAGATGTGCGTACTGACGAGGAAAGGCAGGAGAAGTTCTTGGAA[G/A]
GCTTAAAGGATGAACTGTCAGTTACGTTAATCTCCCATGACTATGTTGATTTTCAGCAGCTGGTTGACAAAGCAATTCGCCTTGAAGACAAGAAGAACAG
Reverse complement sequence
CTGTTCTTCTTGTCTTCAAGGCGAATTGCTTTGTCAACCAGCTGCTGAAAATCAACATAGTCATGGGAGATTAACGTAACTGACAGTTCATCCTTTAAGC[C/T]
TTCCAAGAACTTCTCCTGCCTTTCCTCGTCAGTACGCACATCTTCTGGAGCATAACGTGCCAAACGATTGAACTCATGAAGATACTCTGCCACGGTATGA
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 | 38.90% | 0.60% | 20.14% | 40.44% | NA |
| All Indica | 2759 | 38.10% | 0.00% | 22.04% | 39.91% | NA |
| All Japonica | 1512 | 42.50% | 1.60% | 7.21% | 48.74% | NA |
| Aus | 269 | 30.10% | 0.00% | 60.97% | 8.92% | NA |
| Indica I | 595 | 14.60% | 0.00% | 14.96% | 70.42% | NA |
| Indica II | 465 | 47.50% | 0.00% | 21.08% | 31.40% | NA |
| Indica III | 913 | 46.30% | 0.00% | 26.94% | 26.73% | NA |
| Indica Intermediate | 786 | 40.60% | 0.00% | 22.26% | 37.15% | NA |
| Temperate Japonica | 767 | 73.50% | 2.90% | 4.43% | 19.17% | NA |
| Tropical Japonica | 504 | 3.60% | 0.00% | 11.71% | 84.72% | NA |
| Japonica Intermediate | 241 | 24.90% | 0.80% | 6.64% | 67.63% | NA |
| VI/Aromatic | 96 | 19.80% | 0.00% | 61.46% | 18.75% | NA |
| Intermediate | 90 | 50.00% | 2.20% | 13.33% | 34.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666112 | G -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1212666112 | G -> A | LOC_Os12g22430.1 | missense_variant ; p.Gly193Ser; MODERATE | nonsynonymous_codon ; G193S | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | possibly damaging  |
1.834 |
DELETERIOUS | 0.00 |