| Variant ID: vg0137500139 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 37500139 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGTCCTCAGGAGCCCAGTCCCATCTCACTCCCTGGTGGGTCCTCGTGAAGTCTTCGGACCCGGTGTACTCCCAGGCGCCCCGAGCGCGTCACTGGAGCGG[C/T]
GCAATCCGACGACGGAGGTAGTCGCCGTACACCATGGCCCCTGTGAGCCCCTGGGATCGCAGGCCCGCCAGGCGGTCGAGGACGGCGTCATAGCCATCCC
GGGATGGCTATGACGCCGTCCTCGACCGCCTGGCGGGCCTGCGATCCCAGGGGCTCACAGGGGCCATGGTGTACGGCGACTACCTCCGTCGTCGGATTGC[G/A]
CCGCTCCAGTGACGCGCTCGGGGCGCCTGGGAGTACACCGGGTCCGAAGACTTCACGAGGACCCACCAGGGAGTGAGATGGGACTGGGCTCCTGAGGACT
| 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 | 34.30% | 0.20% | 1.04% | 64.54% | NA |
| All Indica | 2759 | 1.80% | 0.10% | 0.69% | 97.39% | NA |
| All Japonica | 1512 | 93.80% | 0.20% | 1.59% | 4.37% | NA |
| Aus | 269 | 0.70% | 0.00% | 1.86% | 97.40% | NA |
| Indica I | 595 | 1.50% | 0.00% | 0.17% | 98.32% | NA |
| Indica II | 465 | 1.50% | 0.00% | 0.43% | 98.06% | NA |
| Indica III | 913 | 1.20% | 0.10% | 0.44% | 98.25% | NA |
| Indica Intermediate | 786 | 2.80% | 0.40% | 1.53% | 95.29% | NA |
| Temperate Japonica | 767 | 97.90% | 0.00% | 0.52% | 1.56% | NA |
| Tropical Japonica | 504 | 86.90% | 0.40% | 3.37% | 9.33% | NA |
| Japonica Intermediate | 241 | 95.40% | 0.40% | 1.24% | 2.90% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 61.10% | 1.10% | 1.11% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0137500139 | C -> T | LOC_Os01g64600.1 | downstream_gene_variant ; 3254.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0137500139 | C -> T | LOC_Os01g64610.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0137500139 | C -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |