Search for Variation information by Variation ID:
Detailed information for vg0125111765:
| Variant ID: vg0125111765 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 25111765 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGCGCACGCTTATCCGGTCCGTGACCGGTCGCAGTGTGTGACCGGTCAGATCGCGGGTTAGGTGGCAACAGGCGGCCTGTCACACGCCTCGCCCCGTCCC[A/G]
TCGAAATGATGAGAGCCTCCATGCTCTCGTCCCTAGCCGGAGCCGGCGTGTTAACTCCTGGAGTTGGCACGTCAGTCCCGGCCAGATACATTCCAGGCTT
Reverse complement sequence
AAGCCTGGAATGTATCTGGCCGGGACTGACGTGCCAACTCCAGGAGTTAACACGCCGGCTCCGGCTAGGGACGAGAGCATGGAGGCTCTCATCATTTCGA[T/C]
GGGACGGGGCGAGGCGTGTGACAGGCCGCCTGTTGCCACCTAACCCGCGATCTGACCGGTCACACACTGCGACCGGTCACGGACCGGATAAGCGTGCGCT
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 | 17.60% | 0.90% | 6.20% | 75.37% | NA |
| All Indica | 2759 | 1.00% | 1.50% | 9.24% | 88.26% | NA |
| All Japonica | 1512 | 49.70% | 0.00% | 0.20% | 50.07% | NA |
| Aus | 269 | 2.60% | 0.00% | 10.41% | 86.99% | NA |
| Indica I | 595 | 0.50% | 0.20% | 4.37% | 94.96% | NA |
| Indica II | 465 | 1.10% | 0.00% | 12.26% | 86.67% | NA |
| Indica III | 913 | 0.80% | 3.40% | 10.41% | 85.43% | NA |
| Indica Intermediate | 786 | 1.70% | 1.10% | 9.80% | 87.40% | NA |
| Temperate Japonica | 767 | 78.20% | 0.00% | 0.00% | 21.77% | NA |
| Tropical Japonica | 504 | 11.10% | 0.00% | 0.00% | 88.89% | NA |
| Japonica Intermediate | 241 | 39.80% | 0.00% | 1.24% | 58.92% | NA |
| VI/Aromatic | 96 | 18.80% | 0.00% | 1.04% | 80.21% | NA |
| Intermediate | 90 | 27.80% | 0.00% | 6.67% | 65.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0125111765 | A -> G | LOC_Os01g43830.1 | missense_variant ; p.Met95Thr; MODERATE | nonsynonymous_codon ; M95T | Average:15.441; most accessible tissue: Minghui63 panicle, score: 38.588 | benign  |
-0.786 |
TOLERATED | 1.00 |
| vg0125111765 | A -> DEL | LOC_Os01g43830.1 | N | frameshift_variant | Average:15.441; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |