| Variant ID: vg0725374509 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25374509 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.00, others allele: 0.00, population size: 304. )
CTGCCCATACATATACCCCAGTGGTGTTTGAGATCTTTCGTAAAGAGTTTGAGCTGTTCATGGACTCTGTTCTGTTCAGTTGTGGGGAAGCTGGGGCAAC[C/A]
TCTGAGTACAAAGTCGCTCCCTCTGAAAAACCCAAGGAACATTTTGTTAGATTTGACTCGAGTGACTGCTCCTGTATCTGCACTTGTAGGAAGTTTGAGT
ACTCAAACTTCCTACAAGTGCAGATACAGGAGCAGTCACTCGAGTCAAATCTAACAAAATGTTCCTTGGGTTTTTCAGAGGGAGCGACTTTGTACTCAGA[G/T]
GTTGCCCCAGCTTCCCCACAACTGAACAGAACAGAGTCCATGAACAGCTCAAACTCTTTACGAAAGATCTCAAACACCACTGGGGTATATGTATGGGCAG
| 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 | 97.00% | 3.00% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 56.90% | 43.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0725374509 | C -> A | LOC_Os07g42400.1 | synonymous_variant ; p.Thr610Thr; LOW | synonymous_codon | Average:64.92; most accessible tissue: Zhenshan97 panicle, score: 76.605 | N | N | N | N |
| vg0725374509 | C -> A | LOC_Os07g42400.2 | synonymous_variant ; p.Thr610Thr; LOW | synonymous_codon | Average:64.92; most accessible tissue: Zhenshan97 panicle, score: 76.605 | N | N | N | N |