Search for Variation information by Variation ID:
Detailed information for vg1212666253:
| Variant ID: vg1212666253 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666253 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 250. )
Flanking Sequence (100 bp) in Reference Genome:
CTATGTTGATTTTCAGCAGCTGGTTGACAAAGCAATTCGCCTTGAAGACAAGAAGAACAGGATGGATAACCGTAAAAGGAAAATGACTGTTTTCCAGGAG[G/A]
CACAAGGTAGTAGCCAGAGGCAGCGTATCAAGCCACTCCAAATTGGTGAATCTTCTTCCGCTGGTCAAGGACAGTCGCAACTGTTGAACATCGGTGGTGA
Reverse complement sequence
TCACCACCGATGTTCAACAGTTGCGACTGTCCTTGACCAGCGGAAGAAGATTCACCAATTTGGAGTGGCTTGATACGCTGCCTCTGGCTACTACCTTGTG[C/T]
CTCCTGGAAAACAGTCATTTTCCTTTTACGGTTATCCATCCTGTTCTTCTTGTCTTCAAGGCGAATTGCTTTGTCAACCAGCTGCTGAAAATCAACATAG
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 | 71.60% | 0.10% | 7.13% | 21.20% | NA |
| All Indica | 2759 | 75.90% | 0.10% | 6.71% | 17.36% | NA |
| All Japonica | 1512 | 59.50% | 0.10% | 8.66% | 31.68% | NA |
| Aus | 269 | 92.90% | 0.00% | 1.49% | 5.58% | NA |
| Indica I | 595 | 61.20% | 0.00% | 9.75% | 29.08% | NA |
| Indica II | 465 | 77.00% | 0.00% | 6.45% | 16.56% | NA |
| Indica III | 913 | 84.80% | 0.20% | 5.26% | 9.75% | NA |
| Indica Intermediate | 786 | 76.00% | 0.00% | 6.23% | 17.81% | NA |
| Temperate Japonica | 767 | 82.50% | 0.00% | 0.91% | 16.56% | NA |
| Tropical Japonica | 504 | 32.90% | 0.40% | 20.83% | 45.83% | NA |
| Japonica Intermediate | 241 | 41.90% | 0.00% | 7.88% | 50.21% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 8.33% | 12.50% | NA |
| Intermediate | 90 | 71.10% | 0.00% | 10.00% | 18.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666253 | G -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1212666253 | G -> A | LOC_Os12g22430.1 | missense_variant ; p.Ala240Thr; MODERATE | nonsynonymous_codon ; A240T | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | possibly damaging  |
1.571 |
DELETERIOUS | 0.03 |