Search for Variation information by Variation ID:
Detailed information for vg0334132972:
| Variant ID: vg0334132972 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34132972 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 390. )
Flanking Sequence (100 bp) in Reference Genome:
CAGAACTTCGTTGTACCCAGGTTGCGAGCAGGGGCACAAAAAGTTGGATACCACTCTGGAGTTGTTGCAATGGAAGGCAAAAAATGGGGTTAGTGACAAG[G/A]
CATTTGGCGATTTATTGAAACTCGTCAAGAACATTCTTCCGGGGGGAAACAAATTGCCCGAGACAACGTACGAGGCTAAGAAGATAGTCTGCCCGTTAGG
Reverse complement sequence
CCTAACGGGCAGACTATCTTCTTAGCCTCGTACGTTGTCTCGGGCAATTTGTTTCCCCCCGGAAGAATGTTCTTGACGAGTTTCAATAAATCGCCAAATG[C/T]
CTTGTCACTAACCCCATTTTTTGCCTTCCATTGCAACAACTCCAGAGTGGTATCCAACTTTTTGTGCCCCTGCTCGCAACCTGGGTACAACGAAGTTCTG
Allele Frequencies:
| 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 | 7.10% | 0.60% | 18.85% | 73.44% | NA |
| All Indica | 2759 | 11.80% | 0.00% | 29.43% | 58.72% | NA |
| All Japonica | 1512 | 0.10% | 1.20% | 2.51% | 96.16% | NA |
| Aus | 269 | 0.40% | 0.40% | 9.29% | 89.96% | NA |
| Indica I | 595 | 2.20% | 0.00% | 12.61% | 85.21% | NA |
| Indica II | 465 | 16.10% | 0.00% | 29.89% | 53.98% | NA |
| Indica III | 913 | 14.00% | 0.00% | 42.61% | 43.37% | NA |
| Indica Intermediate | 786 | 14.00% | 0.10% | 26.59% | 59.29% | NA |
| Temperate Japonica | 767 | 0.10% | 0.40% | 0.91% | 98.57% | NA |
| Tropical Japonica | 504 | 0.00% | 2.60% | 4.76% | 92.66% | NA |
| Japonica Intermediate | 241 | 0.40% | 0.80% | 2.90% | 95.85% | NA |
| VI/Aromatic | 96 | 1.00% | 7.30% | 2.08% | 89.58% | NA |
| Intermediate | 90 | 5.60% | 2.20% | 15.56% | 76.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0334132972 | G -> A | LOC_Os03g60010.1 | missense_variant ; p.Ala181Thr; MODERATE | nonsynonymous_codon ; A181T | Average:4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 | benign  |
1.244 |
DELETERIOUS | 0.01 |
| vg0334132972 | G -> DEL | LOC_Os03g60010.1 | N | frameshift_variant | Average:4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |