| Variant ID: vg0136520925 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36520925 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATATATGTATGGAAAGATGAAGTACAAAATACTGCGTAGCAAATTCTACCTATGTGTACCCTCTTAATTAAAAAAAAATCATGTGCACTGAAAGAAAAGT[C/T]
AGTATATGCAAAGTTTAGAGAATATTACTGTATGTAAAAAATCAGCATATACCTCTCTATGTAAAAGTGCAGTATATACTTCTTCGTAACAAGGTCCAGT
ACTGGACCTTGTTACGAAGAAGTATATACTGCACTTTTACATAGAGAGGTATATGCTGATTTTTTACATACAGTAATATTCTCTAAACTTTGCATATACT[G/A]
ACTTTTCTTTCAGTGCACATGATTTTTTTTTAATTAAGAGGGTACACATAGGTAGAATTTGCTACGCAGTATTTTGTACTTCATCTTTCCATACATATAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.40% | 0.60% | 3.49% | 60.52% | NA |
| All Indica | 2759 | 2.90% | 0.10% | 1.81% | 95.22% | NA |
| All Japonica | 1512 | 95.70% | 1.40% | 0.26% | 2.65% | NA |
| Aus | 269 | 0.70% | 0.00% | 40.15% | 59.11% | NA |
| Indica I | 595 | 1.30% | 0.00% | 1.51% | 97.14% | NA |
| Indica II | 465 | 3.20% | 0.00% | 1.51% | 95.27% | NA |
| Indica III | 913 | 1.40% | 0.00% | 1.53% | 97.04% | NA |
| Indica Intermediate | 786 | 5.60% | 0.30% | 2.54% | 91.60% | NA |
| Temperate Japonica | 767 | 98.80% | 0.00% | 0.00% | 1.17% | NA |
| Tropical Japonica | 504 | 92.90% | 3.40% | 0.79% | 2.98% | NA |
| Japonica Intermediate | 241 | 91.70% | 1.70% | 0.00% | 6.64% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 1.04% | 6.25% | NA |
| Intermediate | 90 | 63.30% | 3.30% | 2.22% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0136520925 | C -> T | LOC_Os01g63030.1 | downstream_gene_variant ; 4312.0bp to feature; MODIFIER | silent_mutation | Average:4.79; most accessible tissue: Callus, score: 8.026 | N | N | N | N |
| vg0136520925 | C -> T | LOC_Os01g63040.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.79; most accessible tissue: Callus, score: 8.026 | N | N | N | N |
| vg0136520925 | C -> DEL | N | N | silent_mutation | Average:4.79; most accessible tissue: Callus, score: 8.026 | N | N | N | N |