| Variant ID: vg0800164367 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 164367 |
| 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, others allele: 0.00, population size: 80. )
GCACGTCAGCCCCGGCCAGATACATTCCAGGCTTCATCGTAACCATTGCAAGGAAGTCATTGTATGAAGAAGGGCAGACGTGTAGCATGCTAAACTGACA[C/A]
GTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCGCGTCATCGGCAGACAACCGTGCTCCCACGATGCATCTGCCTCCGGTGGAGTGGA
TCCACTCCACCGGAGGCAGATGCATCGTGGGAGCACGGTTGTCTGCCGATGACGCGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCAC[G/T]
TGTCAGTTTAGCATGCTACACGTCTGCCCTTCTTCATACAATGACTTCCTTGCAATGGTTACGATGAAGCCTGGAATGTATCTGGCCGGGGCTGACGTGC
| 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 | 38.30% | 26.30% | 17.37% | 18.01% | NA |
| All Indica | 2759 | 8.60% | 43.90% | 27.36% | 20.12% | NA |
| All Japonica | 1512 | 88.00% | 0.70% | 0.86% | 10.45% | NA |
| Aus | 269 | 67.30% | 3.70% | 9.67% | 19.33% | NA |
| Indica I | 595 | 13.10% | 30.90% | 37.65% | 18.32% | NA |
| Indica II | 465 | 3.90% | 50.50% | 30.11% | 15.48% | NA |
| Indica III | 913 | 7.90% | 47.90% | 20.04% | 24.21% | NA |
| Indica Intermediate | 786 | 8.90% | 45.20% | 26.46% | 19.47% | NA |
| Temperate Japonica | 767 | 97.30% | 0.50% | 0.39% | 1.83% | NA |
| Tropical Japonica | 504 | 73.80% | 1.00% | 1.39% | 23.81% | NA |
| Japonica Intermediate | 241 | 88.40% | 0.40% | 1.24% | 9.96% | NA |
| VI/Aromatic | 96 | 20.80% | 1.00% | 11.46% | 66.67% | NA |
| Intermediate | 90 | 45.60% | 12.20% | 17.78% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0800164367 | C -> A | LOC_Os08g01250.1 | synonymous_variant ; p.Thr39Thr; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0800164367 | C -> DEL | LOC_Os08g01250.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |