| Variant ID: vg0136519161 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36519161 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATGTGTGGAGTAGTTTGTGGGTGTGTGGTATCCCATGGCAGTTGTGTCTCCCCATGGATGGAGAGGACCTTGTATATCCTCAATGGTATCAATAACTTTC[G/A]
TTACTGCTGCCCTTATCGCTATCTTAACTGCCGTTGTAATATTAGTCTTGAAAGCTCTCTTGAATAGGTTAGATGCGTGAATAGCAGTTTGCATGGTGCT
AGCACCATGCAAACTGCTATTCACGCATCTAACCTATTCAAGAGAGCTTTCAAGACTAATATTACAACGGCAGTTAAGATAGCGATAAGGGCAGCAGTAA[C/T]
GAAAGTTATTGATACCATTGAGGATATACAAGGTCCTCTCCATCCATGGGGAGACACAACTGCCATGGGATACCACACACCCACAAACTACTCCACACAT
| 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 | 36.00% | 0.80% | 6.01% | 57.28% | NA |
| All Indica | 2759 | 4.10% | 0.00% | 5.73% | 90.14% | NA |
| All Japonica | 1512 | 94.60% | 2.40% | 0.40% | 2.65% | NA |
| Aus | 269 | 1.90% | 0.00% | 42.38% | 55.76% | NA |
| Indica I | 595 | 2.50% | 0.00% | 3.87% | 93.61% | NA |
| Indica II | 465 | 4.50% | 0.00% | 3.66% | 91.83% | NA |
| Indica III | 913 | 2.60% | 0.00% | 6.90% | 90.47% | NA |
| Indica Intermediate | 786 | 6.90% | 0.00% | 7.00% | 86.13% | NA |
| Temperate Japonica | 767 | 98.80% | 0.00% | 0.00% | 1.17% | NA |
| Tropical Japonica | 504 | 88.70% | 7.10% | 1.19% | 2.98% | NA |
| Japonica Intermediate | 241 | 93.40% | 0.00% | 0.00% | 6.64% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 1.04% | 6.25% | NA |
| Intermediate | 90 | 67.80% | 0.00% | 5.56% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0136519161 | G -> A | LOC_Os01g63040.1 | missense_variant ; p.Thr487Met; MODERATE | nonsynonymous_codon ; T487M | Average:4.671; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 0.06 |
| vg0136519161 | G -> DEL | LOC_Os01g63040.1 | N | frameshift_variant | Average:4.671; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |