| Variant ID: vg0700389102 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 389102 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CAAGGTGGTCATTCAACCGACCCCCTCGCAGGTTCGTCTCATTCTCATTGCGACCACCTTTCTCCCAAAGAGAAGTTTTTTCTTACTCATTTTGTTCGTC[T/C]
TTTGGTTTTTTTTCTTCTGCTTCAGCGATGTCCCGTCGCATTCCTCCCGCCGCCCCAAGTCCGGCCAGTCCGAGGTCGAAGATCCAGCGGCCGCAGAGGA
TCCTCTGCGGCCGCTGGATCTTCGACCTCGGACTGGCCGGACTTGGGGCGGCGGGAGGAATGCGACGGGACATCGCTGAAGCAGAAGAAAAAAAACCAAA[A/G]
GACGAACAAAATGAGTAAGAAAAAACTTCTCTTTGGGAGAAAGGTGGTCGCAATGAGAATGAGACGAACCTGCGAGGGGGTCGGTTGAATGACCACCTTG
| 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 | 38.90% | 0.10% | 3.60% | 57.47% | NA |
| All Indica | 2759 | 14.40% | 0.00% | 1.81% | 83.83% | NA |
| All Japonica | 1512 | 85.80% | 0.20% | 7.01% | 7.01% | NA |
| Aus | 269 | 0.40% | 0.00% | 3.35% | 96.28% | NA |
| Indica I | 595 | 3.20% | 0.00% | 2.86% | 93.95% | NA |
| Indica II | 465 | 55.90% | 0.00% | 0.43% | 43.66% | NA |
| Indica III | 913 | 0.80% | 0.00% | 1.53% | 97.70% | NA |
| Indica Intermediate | 786 | 14.00% | 0.00% | 2.16% | 83.84% | NA |
| Temperate Japonica | 767 | 85.10% | 0.00% | 11.99% | 2.87% | NA |
| Tropical Japonica | 504 | 83.90% | 0.00% | 0.79% | 15.28% | NA |
| Japonica Intermediate | 241 | 91.70% | 1.20% | 4.15% | 2.90% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 0.00% | 10.42% | NA |
| Intermediate | 90 | 63.30% | 0.00% | 5.56% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0700389102 | T -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0700389102 | T -> C | LOC_Os07g01620.1 | downstream_gene_variant ; 4102.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0700389102 | T -> C | LOC_Os07g01650.1 | downstream_gene_variant ; 2537.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0700389102 | T -> C | LOC_Os07g01640.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |