Variant ID: vg1213095434 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 13095434 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 318. )
CTTTTGGACAATAAGTTGATCTAGGGCAAGCAGCAGAAGCTCTAAAATGGATCAGTAGTTGTCGAGGCAAGAAGACAACGATTTCAACCATCAGAATAAA[A/G]
AAGGGCAGCCTCAAACTCCACTCCTGACTTGGCCATGTCCAAAATCAATGTATAAAGGAAAATGGTACACATCGGCCTTCTTTTTGCGGATTGAAGATCA
TGATCTTCAATCCGCAAAAAGAAGGCCGATGTGTACCATTTTCCTTTATACATTGATTTTGGACATGGCCAAGTCAGGAGTGGAGTTTGAGGCTGCCCTT[T/C]
TTTATTCTGATGGTTGAAATCGTTGTCTTCTTGCCTCGACAACTACTGATCCATTTTAGAGCTTCTGCTGCTTGCCCTAGATCAACTTATTGTCCAAAAG
Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 88.80% | 0.00% | 0.47% | 10.75% | NA |
All Indica | 2759 | 82.20% | 0.00% | 0.76% | 17.04% | NA |
All Japonica | 1512 | 97.60% | 0.00% | 0.07% | 2.31% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 98.80% | 0.00% | 0.17% | 1.01% | NA |
Indica II | 465 | 60.90% | 0.00% | 2.15% | 36.99% | NA |
Indica III | 913 | 81.80% | 0.10% | 0.66% | 17.42% | NA |
Indica Intermediate | 786 | 82.60% | 0.00% | 0.51% | 16.92% | NA |
Temperate Japonica | 767 | 95.80% | 0.00% | 0.13% | 4.04% | NA |
Tropical Japonica | 504 | 99.60% | 0.00% | 0.00% | 0.40% | NA |
Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 96.70% | 0.00% | 0.00% | 3.33% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1213095434 | A -> DEL | LOC_Os12g23150.1 | N | frameshift_variant | Average:65.526; most accessible tissue: Zhenshan97 young leaf, score: 80.589 | N | N | N | N |
vg1213095434 | A -> G | LOC_Os12g23150.1 | missense_variant ; p.Phe231Leu; MODERATE | nonsynonymous_codon ; F231L | Average:65.526; most accessible tissue: Zhenshan97 young leaf, score: 80.589 | unknown | unknown | DELETERIOUS | 0.00 |