Search for Variation information by Variation ID:
Detailed information for vg1126363031:
| Variant ID: vg1126363031 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26363031 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 200. )
Flanking Sequence (100 bp) in Reference Genome:
CAGGAGGCAGGAACGCCGTGAGGGCAAGTCTGCGGCAGTTCCCTCCGGTAAACGGCGAAGTGAGGCCAGACAGAAGGCCCCCGCCGTTGACATCGATGAT[G/A]
GTGATGATGACCTAGGTTTCCAAGAACCTGGGGCCACCATTGCCACTGTCGACGGGGGAGCGTGTGCTCACGTTTCTCGCCGGAGTTTCAAGGCCATGAG
Reverse complement sequence
CTCATGGCCTTGAAACTCCGGCGAGAAACGTGAGCACACGCTCCCCCGTCGACAGTGGCAATGGTGGCCCCAGGTTCTTGGAAACCTAGGTCATCATCAC[C/T]
ATCATCGATGTCAACGGCGGGGGCCTTCTGTCTGGCCTCACTTCGCCGTTTACCGGAGGGAACTGCCGCAGACTTGCCCTCACGGCGTTCCTGCCTCCTG
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 | 29.30% | 0.00% | 21.71% | 48.92% | NA |
| All Indica | 2759 | 12.80% | 0.00% | 23.31% | 63.90% | NA |
| All Japonica | 1512 | 54.20% | 0.10% | 18.85% | 26.79% | NA |
| Aus | 269 | 36.40% | 0.00% | 28.25% | 35.32% | NA |
| Indica I | 595 | 7.40% | 0.00% | 8.91% | 83.70% | NA |
| Indica II | 465 | 7.30% | 0.00% | 17.85% | 74.84% | NA |
| Indica III | 913 | 15.10% | 0.00% | 37.24% | 47.65% | NA |
| Indica Intermediate | 786 | 17.40% | 0.00% | 21.25% | 61.32% | NA |
| Temperate Japonica | 767 | 49.20% | 0.30% | 17.08% | 33.51% | NA |
| Tropical Japonica | 504 | 58.10% | 0.00% | 21.63% | 20.24% | NA |
| Japonica Intermediate | 241 | 62.20% | 0.00% | 18.67% | 19.09% | NA |
| VI/Aromatic | 96 | 78.10% | 0.00% | 13.54% | 8.33% | NA |
| Intermediate | 90 | 44.40% | 0.00% | 10.00% | 45.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126363031 | G -> A | LOC_Os11g43670.1 | missense_variant ; p.Gly538Ser; MODERATE | nonsynonymous_codon ; G538S | Average:12.881; most accessible tissue: Minghui63 panicle, score: 25.313 | possibly damaging  |
1.975 |
DELETERIOUS | 0.01 |
| vg1126363031 | G -> DEL | LOC_Os11g43670.1 | N | frameshift_variant | Average:12.881; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |