Search for Variation information by Variation ID:
Detailed information for vg0625554578:
| Variant ID: vg0625554578 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 25554578 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGTGAATGTCTCGAGCATTGTGGTCCACAGCATCTCTTTCTCCGAATCTGGGACAAAGCTCTCATGATCTCCGTGTGCCCTTGTTCTTCGCCAGTACACC[G/A]
TACTGACAGGCACGTTATCCCGCACAACCCAACCGCTGTGACGTACATAGTTCTTGGTGGCTTCGGCTGGGGCACTAGGACGTCCATCTTCTTCCACTTC
Reverse complement sequence
GAAGTGGAAGAAGATGGACGTCCTAGTGCCCCAGCCGAAGCCACCAAGAACTATGTACGTCACAGCGGTTGGGTTGTGCGGGATAACGTGCCTGTCAGTA[C/T]
GGTGTACTGGCGAAGAACAAGGGCACACGGAGATCATGAGAGCTTTGTCCCAGATTCGGAGAAAGAGATGCTGTGGACCACAATGCTCGAGACATTCACC
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 | 70.00% | 0.10% | 5.82% | 24.12% | NA |
| All Indica | 2759 | 81.70% | 0.10% | 6.23% | 11.92% | NA |
| All Japonica | 1512 | 52.70% | 0.00% | 2.91% | 44.38% | NA |
| Aus | 269 | 54.30% | 0.00% | 13.01% | 32.71% | NA |
| Indica I | 595 | 62.40% | 0.00% | 11.09% | 26.55% | NA |
| Indica II | 465 | 85.20% | 0.00% | 6.45% | 8.39% | NA |
| Indica III | 913 | 95.10% | 0.30% | 1.97% | 2.63% | NA |
| Indica Intermediate | 786 | 78.80% | 0.10% | 7.38% | 13.74% | NA |
| Temperate Japonica | 767 | 65.30% | 0.00% | 0.91% | 33.77% | NA |
| Tropical Japonica | 504 | 34.70% | 0.00% | 5.16% | 60.12% | NA |
| Japonica Intermediate | 241 | 50.20% | 0.00% | 4.56% | 45.23% | NA |
| VI/Aromatic | 96 | 51.00% | 0.00% | 16.67% | 32.29% | NA |
| Intermediate | 90 | 67.80% | 0.00% | 8.89% | 23.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0625554578 | G -> A | LOC_Os06g42500.1 | missense_variant ; p.Thr128Met; MODERATE | nonsynonymous_codon ; T128M | Average:15.59; most accessible tissue: Minghui63 young leaf, score: 22.423 | benign  |
0.722 |
DELETERIOUS | 0.02 |
| vg0625554578 | G -> DEL | LOC_Os06g42500.1 | N | frameshift_variant | Average:15.59; most accessible tissue: Minghui63 young leaf, score: 22.423 | N | N | N | N |