| Variant ID: vg1209004419 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9004419 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCGCCGGAAGTGAAGACATGGTCGCCATCAACAACGGCAGCGGATTACACCAACCGTGGAGGCGAAGAAACCGGTCGGCAGTGATGACGGCGGCCAGCGA[T/C]
GAAGGTGTAGATGCCCAACAACGGTGGTGTGACCAACCAACCGTGTAGGCGAGGACACTAGTTGACAGTGGACGAGGCGGCCGGTCAGTGAAGACGATGA
TCATCGTCTTCACTGACCGGCCGCCTCGTCCACTGTCAACTAGTGTCCTCGCCTACACGGTTGGTTGGTCACACCACCGTTGTTGGGCATCTACACCTTC[A/G]
TCGCTGGCCGCCGTCATCACTGCCGACCGGTTTCTTCGCCTCCACGGTTGGTGTAATCCGCTGCCGTTGTTGATGGCGACCATGTCTTCACTTCCGGCGG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 79.30% | 0.60% | 1.12% | 18.98% | NA |
| All Indica | 2759 | 66.80% | 0.90% | 1.81% | 30.48% | NA |
| All Japonica | 1512 | 99.10% | 0.00% | 0.07% | 0.86% | NA |
| Aus | 269 | 87.40% | 0.40% | 0.37% | 11.90% | NA |
| Indica I | 595 | 63.00% | 0.20% | 3.19% | 33.61% | NA |
| Indica II | 465 | 67.10% | 0.00% | 1.29% | 31.61% | NA |
| Indica III | 913 | 68.00% | 1.80% | 1.64% | 28.59% | NA |
| Indica Intermediate | 786 | 67.90% | 1.10% | 1.27% | 29.64% | NA |
| Temperate Japonica | 767 | 99.10% | 0.00% | 0.00% | 0.91% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.20% | 0.60% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 1.04% | 4.17% | NA |
| Intermediate | 90 | 92.20% | 0.00% | 0.00% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209004419 | T -> C | LOC_Os12g15770.1 | synonymous_variant ; p.Ser73Ser; LOW | synonymous_codon | Average:40.772; most accessible tissue: Zhenshan97 young leaf, score: 69.723 | N | N | N | N |
| vg1209004419 | T -> DEL | LOC_Os12g15770.1 | N | frameshift_variant | Average:40.772; most accessible tissue: Zhenshan97 young leaf, score: 69.723 | N | N | N | N |