| Variant ID: vg0221509629 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21509629 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GAACTTGCCACCCGCGTCCGTCCACTCTTGGGAGGATTTGTGCCAACAGTTCACCATGAACTTTCAAGGCACATATCCGTGCCCAGGTGAAGAAGCGGAC[C/T]
TGCACGCAGTACAGCGAAGGGATGATGAGTCACTTCGCTCGTACATTCAGCGGTTCTGTCAAGTCCGCAACACCATACCAAGCATCCCTGCACACGCGGT
ACCGCGTGTGCAGGGATGCTTGGTATGGTGTTGCGGACTTGACAGAACCGCTGAATGTACGAGCGAAGTGACTCATCATCCCTTCGCTGTACTGCGTGCA[G/A]
GTCCGCTTCTTCACCTGGGCACGGATATGTGCCTTGAAAGTTCATGGTGAACTGTTGGCACAAATCCTCCCAAGAGTGGACGGACGCGGGTGGCAAGTTC
| 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 | 40.60% | 0.30% | 6.81% | 52.29% | NA |
| All Indica | 2759 | 5.10% | 0.40% | 7.94% | 86.55% | NA |
| All Japonica | 1512 | 98.10% | 0.00% | 1.19% | 0.66% | NA |
| Aus | 269 | 52.40% | 0.00% | 26.77% | 20.82% | NA |
| Indica I | 595 | 5.20% | 0.00% | 12.77% | 82.02% | NA |
| Indica II | 465 | 4.70% | 0.00% | 8.60% | 86.67% | NA |
| Indica III | 913 | 3.30% | 1.30% | 1.86% | 93.54% | NA |
| Indica Intermediate | 786 | 7.30% | 0.00% | 10.94% | 81.81% | NA |
| Temperate Japonica | 767 | 99.00% | 0.00% | 0.78% | 0.26% | NA |
| Tropical Japonica | 504 | 96.80% | 0.00% | 1.59% | 1.59% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 70.00% | 0.00% | 11.11% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221509629 | C -> T | LOC_Os02g35800.1 | synonymous_variant ; p.Leu323Leu; LOW | synonymous_codon | Average:4.785; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0221509629 | C -> DEL | LOC_Os02g35800.1 | N | frameshift_variant | Average:4.785; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |