| Variant ID: vg0724212644 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 24212644 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 309. )
TTAGTGTTCTAGCTTTATTATCCATGTAACTCTGGAGTGATGAGGGAACAGCATGTCGATCCTGGCATCTTCAGGTGTAGGTTCTCTAGTAGGTTCAGAT[C/A]
GAATCGGCTGGCGTTGCGTACCTTGCGTTCGTGCATCTATGCACCGGTGTATCCTTTTCAATCGTTGAACTACTGGATCGTTTGATGCAAGCGAATATTT
AAATATTCGCTTGCATCAAACGATCCAGTAGTTCAACGATTGAAAAGGATACACCGGTGCATAGATGCACGAACGCAAGGTACGCAACGCCAGCCGATTC[G/T]
ATCTGAACCTACTAGAGAACCTACACCTGAAGATGCCAGGATCGACATGCTGTTCCCTCATCACTCCAGAGTTACATGGATAATAAAGCTAGAACACTAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.80% | 3.80% | 0.36% | 0.00% | NA |
| All Indica | 2759 | 92.90% | 6.50% | 0.62% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.00% | 0.50% | 0.00% | NA |
| Indica II | 465 | 94.00% | 5.20% | 0.86% | 0.00% | NA |
| Indica III | 913 | 85.70% | 14.00% | 0.33% | 0.00% | NA |
| Indica Intermediate | 786 | 95.70% | 3.40% | 0.89% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0724212644 | C -> A | LOC_Os07g40380.1 | 3_prime_UTR_variant ; 300.0bp to feature; MODIFIER | silent_mutation | Average:72.482; most accessible tissue: Callus, score: 98.501 | N | N | N | N |
| vg0724212644 | C -> A | LOC_Os07g40370.1 | upstream_gene_variant ; 4679.0bp to feature; MODIFIER | silent_mutation | Average:72.482; most accessible tissue: Callus, score: 98.501 | N | N | N | N |
| vg0724212644 | C -> A | LOC_Os07g40390.1 | downstream_gene_variant ; 3234.0bp to feature; MODIFIER | silent_mutation | Average:72.482; most accessible tissue: Callus, score: 98.501 | N | N | N | N |