| Variant ID: vg0814380312 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 14380312 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCGCCCTTCTCTTCAGCTGTTCCGGTGGTTCTTCACCGTGCAGTCGGTGTCACCGCCGTCGGTGGTTGGCGGCTGCTACTTCCAGCCGCGGGGGCCGGTG[T/C]
TGAACCGCTACATCCCTTGCGTCCTCCGCAAGAAGTGGGACGACTGGAAGAGCGACTGGTTCTACACCCCCCTCGCCAACGAAGCGCGCCTCCGACTTCC
GGAAGTCGGAGGCGCGCTTCGTTGGCGAGGGGGGTGTAGAACCAGTCGCTCTTCCAGTCGTCCCACTTCTTGCGGAGGACGCAAGGGATGTAGCGGTTCA[A/G]
CACCGGCCCCCGCGGCTGGAAGTAGCAGCCGCCAACCACCGACGGCGGTGACACCGACTGCACGGTGAAGAACCACCGGAACAGCTGAAGAGAAGGGCGC
| 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 | 0.20% | 0.10% | 2.39% | 97.27% | NA |
| All Indica | 2759 | 0.30% | 0.00% | 0.65% | 98.99% | NA |
| All Japonica | 1512 | 0.00% | 0.30% | 6.08% | 93.58% | NA |
| Aus | 269 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Indica I | 595 | 0.20% | 0.00% | 0.17% | 99.66% | NA |
| Indica II | 465 | 0.00% | 0.00% | 0.43% | 99.57% | NA |
| Indica III | 913 | 0.50% | 0.10% | 0.99% | 98.36% | NA |
| Indica Intermediate | 786 | 0.40% | 0.00% | 0.76% | 98.85% | NA |
| Temperate Japonica | 767 | 0.00% | 0.50% | 10.56% | 88.92% | NA |
| Tropical Japonica | 504 | 0.00% | 0.00% | 0.60% | 99.40% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.40% | 3.32% | 96.27% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 0.00% | 1.10% | 3.33% | 95.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0814380312 | T -> C | LOC_Os08g23760.1 | synonymous_variant ; p.Leu144Leu; LOW | synonymous_codon | Average:13.423; most accessible tissue: Minghui63 young leaf, score: 23.613 | N | N | N | N |
| vg0814380312 | T -> DEL | LOC_Os08g23760.1 | N | frameshift_variant | Average:13.423; most accessible tissue: Minghui63 young leaf, score: 23.613 | N | N | N | N |