| Variant ID: vg1023166353 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 23166353 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 295. )
TGAAAATTTCAGCAGGTTCTATAGGACATGGGGTAGTCAACACCCAGTCCACCTCTCCCAAGATAAAGGCAAGGTCGAGTTCTCTTTTCCATTCTTCGTA[G/A]
TTATCTCCTTTCAGGGTCGGAATATCTTTAATGTAACCCATCAAGGAGTAGCCACCTGAGATAATCATGTATTGTGAGAACAAAATTAACATTAAAATTA
TAATTTTAATGTTAATTTTGTTCTCACAATACATGATTATCTCAGGTGGCTACTCCTTGATGGGTTACATTAAAGATATTCCGACCCTGAAAGGAGATAA[C/T]
TACGAAGAATGGAAAAGAGAACTCGACCTTGCCTTTATCTTGGGAGAGGTGGACTGGGTGTTGACTACCCCATGTCCTATAGAACCTGCTGAAATTTTCA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 76.10% | 2.50% | 8.84% | 12.59% | NA |
| All Indica | 2759 | 62.60% | 3.90% | 13.16% | 20.33% | NA |
| All Japonica | 1512 | 99.20% | 0.00% | 0.60% | 0.20% | NA |
| Aus | 269 | 73.60% | 3.00% | 15.24% | 8.18% | NA |
| Indica I | 595 | 42.40% | 3.90% | 16.64% | 37.14% | NA |
| Indica II | 465 | 50.30% | 5.60% | 15.70% | 28.39% | NA |
| Indica III | 913 | 84.70% | 2.50% | 7.67% | 5.15% | NA |
| Indica Intermediate | 786 | 59.50% | 4.60% | 15.39% | 20.48% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 98.00% | 0.00% | 1.59% | 0.40% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 1.04% | 1.04% | NA |
| Intermediate | 90 | 84.40% | 2.20% | 4.44% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1023166353 | G -> A | LOC_Os10g42980.1 | synonymous_variant ; p.Asn28Asn; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166353 | G -> DEL | LOC_Os10g42980.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |