| Variant ID: vg0800164184 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 164184 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGCATAGCGCATGCTTATCCGGTCCGTGATCGGTCGCAGTGTGTGACCGGTCACAGACCGGTCAGATCGCGGGTTAGGGGGCAACAGGCGGCCTGACACA[C/T]
GCCTCGCCCCGTCCCGTCGGAATGATGAGAGCCTCCAGGCACTCGTCCCTAGCCGGAGCCGGCGTGGGAACTCCTAGAGTTGGCACGTCAGCCCCGGCCA
TGGCCGGGGCTGACGTGCCAACTCTAGGAGTTCCCACGCCGGCTCCGGCTAGGGACGAGTGCCTGGAGGCTCTCATCATTCCGACGGGACGGGGCGAGGC[G/A]
TGTGTCAGGCCGCCTGTTGCCCCCTAACCCGCGATCTGACCGGTCTGTGACCGGTCACACACTGCGACCGATCACGGACCGGATAAGCATGCGCTATGCT
| 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 | 31.60% | 0.70% | 4.99% | 62.63% | NA |
| All Indica | 2759 | 5.50% | 0.10% | 4.20% | 90.25% | NA |
| All Japonica | 1512 | 84.90% | 2.10% | 1.39% | 11.57% | NA |
| Aus | 269 | 3.30% | 0.00% | 33.83% | 62.83% | NA |
| Indica I | 595 | 12.80% | 0.00% | 2.02% | 85.21% | NA |
| Indica II | 465 | 3.90% | 0.00% | 4.30% | 91.83% | NA |
| Indica III | 913 | 1.60% | 0.00% | 5.26% | 93.10% | NA |
| Indica Intermediate | 786 | 5.30% | 0.30% | 4.58% | 89.82% | NA |
| Temperate Japonica | 767 | 93.00% | 4.20% | 0.26% | 2.61% | NA |
| Tropical Japonica | 504 | 71.00% | 0.00% | 3.77% | 25.20% | NA |
| Japonica Intermediate | 241 | 88.40% | 0.00% | 0.00% | 11.62% | NA |
| VI/Aromatic | 96 | 13.50% | 0.00% | 2.08% | 84.38% | NA |
| Intermediate | 90 | 42.20% | 1.10% | 6.67% | 50.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0800164184 | C -> T | LOC_Os08g01250.1 | synonymous_variant ; p.Ala100Ala; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0800164184 | C -> DEL | LOC_Os08g01250.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |