| Variant ID: vg1221990008 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 21990008 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCCACACGTACAGGAGTCGGATGAGGAGCAAGAGAGATACCGAGGCGAAGATTGCAGACCTAGAGTTCCGGGTATCGAGCTACGAACTCAACATGCAAGA[G/A]
GAGGTGGCAAGGAAGGTTGATGAACGCATGGCCGCACATCGGTCCCATGATCCCCAGCCGACCATTCCTCCTGCAATGGTGAGTCCGTCAGGAAACCGTA
TACGGTTTCCTGACGGACTCACCATTGCAGGAGGAATGGTCGGCTGGGGATCATGGGACCGATGTGCGGCCATGCGTTCATCAACCTTCCTTGCCACCTC[C/T]
TCTTGCATGTTGAGTTCGTAGCTCGATACCCGGAACTCTAGGTCTGCAATCTTCGCCTCGGTATCTCTCTTGCTCCTCATCCGACTCCTGTACGTGTGGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.80% | 0.20% | 2.98% | 30.00% | NA |
| All Indica | 2759 | 54.40% | 0.30% | 2.90% | 42.33% | NA |
| All Japonica | 1512 | 91.30% | 0.00% | 0.13% | 8.60% | NA |
| Aus | 269 | 45.40% | 0.00% | 14.50% | 40.15% | NA |
| Indica I | 595 | 68.70% | 0.00% | 0.67% | 30.59% | NA |
| Indica II | 465 | 72.90% | 0.00% | 0.86% | 26.24% | NA |
| Indica III | 913 | 32.50% | 1.00% | 5.91% | 60.57% | NA |
| Indica Intermediate | 786 | 58.10% | 0.00% | 2.29% | 39.57% | NA |
| Temperate Japonica | 767 | 96.50% | 0.00% | 0.13% | 3.39% | NA |
| Tropical Japonica | 504 | 80.20% | 0.00% | 0.20% | 19.64% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 82.30% | 0.00% | 16.67% | 1.04% | NA |
| Intermediate | 90 | 83.30% | 0.00% | 4.44% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1221990008 | G -> DEL | LOC_Os12g35970.1 | N | frameshift_variant | Average:10.505; most accessible tissue: Minghui63 flag leaf, score: 17.021 | N | N | N | N |
| vg1221990008 | G -> A | LOC_Os12g35970.1 | synonymous_variant ; p.Glu86Glu; LOW | stop_gained | Average:10.505; most accessible tissue: Minghui63 flag leaf, score: 17.021 | N | N | N | N |