| Variant ID: vg0139513562 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39513562 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 254. )
CTCGTTCCATACTCCCAAACTGCAACTCTCCTATCGCTCGCAGAATGCCAGCGTGCCTATCATGTATCAGGCATACATTTGGCCTCATACCAACAACTTT[T/G]
GTTTTAACCAATTTCAGGAACCAGTACCAGCTGTCGGTATTCTCACTCTCAACAAAAGCAAATGCCAAGGGCAATACCTGATTGTTCCCATCTACCCCTA
TAGGGGTAGATGGGAACAATCAGGTATTGCCCTTGGCATTTGCTTTTGTTGAGAGTGAGAATACCGACAGCTGGTACTGGTTCCTGAAATTGGTTAAAAC[A/C]
AAAGTTGTTGGTATGAGGCCAAATGTATGCCTGATACATGATAGGCACGCTGGCATTCTGCGAGCGATAGGAGAGTTGCAGTTTGGGAGTATGGAACGAG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 26.20% | 1.00% | 1.16% | 71.67% | NA |
| All Indica | 2759 | 2.60% | 0.40% | 1.30% | 95.65% | NA |
| All Japonica | 1512 | 74.50% | 0.30% | 0.40% | 24.87% | NA |
| Aus | 269 | 0.00% | 2.20% | 2.97% | 94.80% | NA |
| Indica I | 595 | 2.70% | 0.00% | 2.35% | 94.96% | NA |
| Indica II | 465 | 1.10% | 0.00% | 0.00% | 98.92% | NA |
| Indica III | 913 | 1.40% | 1.00% | 1.64% | 95.95% | NA |
| Indica Intermediate | 786 | 5.00% | 0.30% | 0.89% | 93.89% | NA |
| Temperate Japonica | 767 | 97.10% | 0.00% | 0.13% | 2.74% | NA |
| Tropical Japonica | 504 | 52.20% | 0.00% | 0.99% | 46.83% | NA |
| Japonica Intermediate | 241 | 49.00% | 1.70% | 0.00% | 49.38% | NA |
| VI/Aromatic | 96 | 1.00% | 24.00% | 4.17% | 70.83% | NA |
| Intermediate | 90 | 40.00% | 4.40% | 1.11% | 54.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139513562 | T -> G | LOC_Os01g67990.1 | synonymous_variant ; p.Thr444Thr; LOW | synonymous_codon | Average:5.54; most accessible tissue: Callus, score: 16.271 | N | N | N | N |
| vg0139513562 | T -> DEL | LOC_Os01g67990.1 | N | frameshift_variant | Average:5.54; most accessible tissue: Callus, score: 16.271 | N | N | N | N |