| Variant ID: vg0424679374 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24679374 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGACTAAAATAGTCATGTATATGCTAAGTGTTTCGTGCGTATATGCTAAGTCTAATTAAGACTACAATAGTCAATTGCTACTTGTCGCACCAATTCCGTA[G/T]
TCAATAATTACATACCAAGTCTAATTACAAATAAAGTAATATTATATTAAAACTCAAATAATATTACATGCTAAGACTAAAATAGTAATGTATGCTAAGT
ACTTAGCATACATTACTATTTTAGTCTTAGCATGTAATATTATTTGAGTTTTAATATAATATTACTTTATTTGTAATTAGACTTGGTATGTAATTATTGA[C/A]
TACGGAATTGGTGCGACAAGTAGCAATTGACTATTGTAGTCTTAATTAGACTTAGCATATACGCACGAAACACTTAGCATATACATGACTATTTTAGTCT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.50% | 0.10% | 2.09% | 54.25% | NA |
| All Indica | 2759 | 6.70% | 0.10% | 3.19% | 90.00% | NA |
| All Japonica | 1512 | 99.30% | 0.10% | 0.13% | 0.46% | NA |
| Aus | 269 | 81.00% | 0.00% | 1.12% | 17.84% | NA |
| Indica I | 595 | 4.70% | 0.00% | 1.51% | 93.78% | NA |
| Indica II | 465 | 4.90% | 0.00% | 3.44% | 91.61% | NA |
| Indica III | 913 | 6.20% | 0.20% | 4.38% | 89.16% | NA |
| Indica Intermediate | 786 | 9.80% | 0.10% | 2.93% | 87.15% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 99.00% | 0.00% | 0.20% | 0.79% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.40% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 62.20% | 2.20% | 6.67% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424679374 | G -> DEL | N | N | silent_mutation | Average:5.808; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |
| vg0424679374 | G -> T | LOC_Os04g41599.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.808; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |