| Variant ID: vg0142999498 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 42999498 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTTGATTATGCAAGATTTGACCGAGGGGGTAAGACGTAACTACTGTGACCCGATGCGCCTGGAAATAATGGCGCAGTTTCCTCGAGGCCATTAGAATAGC[G/A]
TAAAGCATCTTCTGGGCCTGAGGGTATCGGGTTTTGGCGTCCCGGAGGGCCTCACTAACAAAGTAGACGGGCCGCTGCACCTTTCGGTGGGGCCGATCCT
AGGATCGGCCCCACCGAAAGGTGCAGCGGCCCGTCTACTTTGTTAGTGAGGCCCTCCGGGACGCCAAAACCCGATACCCTCAGGCCCAGAAGATGCTTTA[C/T]
GCTATTCTAATGGCCTCGAGGAAACTGCGCCATTATTTCCAGGCGCATCGGGTCACAGTAGTTACGTCTTACCCCCTCGGTCAAATCTTGCATAATCAAG
| 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 | 15.00% | 0.10% | 8.29% | 76.58% | NA |
| All Indica | 2759 | 9.60% | 0.20% | 9.68% | 80.50% | NA |
| All Japonica | 1512 | 21.10% | 0.10% | 3.57% | 75.26% | NA |
| Aus | 269 | 37.90% | 0.00% | 12.64% | 49.44% | NA |
| Indica I | 595 | 5.90% | 0.00% | 4.37% | 89.75% | NA |
| Indica II | 465 | 3.90% | 0.20% | 5.59% | 90.32% | NA |
| Indica III | 913 | 14.50% | 0.30% | 17.09% | 68.13% | NA |
| Indica Intermediate | 786 | 10.20% | 0.30% | 7.51% | 82.06% | NA |
| Temperate Japonica | 767 | 38.70% | 0.00% | 0.39% | 60.89% | NA |
| Tropical Japonica | 504 | 2.40% | 0.00% | 8.73% | 88.89% | NA |
| Japonica Intermediate | 241 | 4.10% | 0.40% | 2.90% | 92.53% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 28.12% | 67.71% | NA |
| Intermediate | 90 | 20.00% | 0.00% | 11.11% | 68.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0142999498 | G -> A | LOC_Os01g74230.1 | synonymous_variant ; p.Tyr1168Tyr; LOW | synonymous_codon | Average:7.978; most accessible tissue: Callus, score: 15.971 | N | N | N | N |
| vg0142999498 | G -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:7.978; most accessible tissue: Callus, score: 15.971 | N | N | N | N |