| Variant ID: vg1021202569 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 21202569 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.02, others allele: 0.00, population size: 281. )
GCGCATTCCTCCTACCCTTGTAAGTATGTTTCTAGAGTTCAATTTCCATTGTGTATCAGGCCACTTTCATCAATTGCAGGGTCACACTGACAAAGTTGTT[T/C]
GAAATCTTCTATACAATTATCTTCCTTGTCTTTTTAGCACAAATATCCGACATCCATTTTTTCTATTTCAATGAATGAAAACATTTCCTAAGATGGATCT
AGATCCATCTTAGGAAATGTTTTCATTCATTGAAATAGAAAAAATGGATGTCGGATATTTGTGCTAAAAAGACAAGGAAGATAATTGTATAGAAGATTTC[A/G]
AACAACTTTGTCAGTGTGACCCTGCAATTGATGAAAGTGGCCTGATACACAATGGAAATTGAACTCTAGAAACATACTTACAAGGGTAGGAGGAATGCGC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.70% | 6.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 98.40% | 1.60% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 11.50% | 88.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 91.70% | 8.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1021202569 | T -> C | LOC_Os10g39680.1 | upstream_gene_variant ; 3131.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1021202569 | T -> C | LOC_Os10g39670.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |