| Variant ID: vg1209004386 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9004386 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCCAATAAAAACACCAGTCGGCGGCGATGGCAGCCGCCGGAAGTGAAGACATGGTCGCCATCAACAACGGCAGCGGATTACACCAACCGTGGAGGCGAAG[A/C]
AACCGGTCGGCAGTGATGACGGCGGCCAGCGATGAAGGTGTAGATGCCCAACAACGGTGGTGTGACCAACCAACCGTGTAGGCGAGGACACTAGTTGACA
TGTCAACTAGTGTCCTCGCCTACACGGTTGGTTGGTCACACCACCGTTGTTGGGCATCTACACCTTCATCGCTGGCCGCCGTCATCACTGCCGACCGGTT[T/G]
CTTCGCCTCCACGGTTGGTGTAATCCGCTGCCGTTGTTGATGGCGACCATGTCTTCACTTCCGGCGGCTGCCATCGCCGCCGACTGGTGTTTTTATTGGG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.70% | 0.90% | 1.18% | 20.23% | NA |
| All Indica | 2759 | 65.70% | 0.10% | 1.59% | 32.58% | NA |
| All Japonica | 1512 | 99.00% | 0.00% | 0.07% | 0.93% | NA |
| Aus | 269 | 69.10% | 14.90% | 4.09% | 11.90% | NA |
| Indica I | 595 | 58.00% | 0.00% | 3.03% | 38.99% | NA |
| Indica II | 465 | 66.50% | 0.00% | 0.86% | 32.69% | NA |
| Indica III | 913 | 68.90% | 0.10% | 1.10% | 29.90% | NA |
| Indica Intermediate | 786 | 67.60% | 0.10% | 1.53% | 30.79% | NA |
| Temperate Japonica | 767 | 99.10% | 0.00% | 0.00% | 0.91% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.41% | 1.66% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1209004386 | A -> C | LOC_Os12g15770.1 | missense_variant ; p.Phe84Leu; MODERATE | nonsynonymous_codon ; F84L | Average:39.813; most accessible tissue: Minghui63 young leaf, score: 66.656 | unknown | unknown | TOLERATED | 0.69 |
| vg1209004386 | A -> DEL | LOC_Os12g15770.1 | N | frameshift_variant | Average:39.813; most accessible tissue: Minghui63 young leaf, score: 66.656 | N | N | N | N |