| Variant ID: vg0101920381 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 1920381 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 363. )
CGGTATACAGACGGAAGACGTGACATAGTTTCCAACCCATCCTAGCCATAGACAAGAGTACCGACCCAATCCCACCTACGGCCGGAACCCCCGGGACAGG[C/T]
AGGCAGGACTGAGCCCCTAGCAGCAGGACACCGGCCCTGTGCCATGACATCTCGACTACCGGGCCGCAGCTCGTGTAGCCTTCATTTGCCCTGGAGAATG
CATTCTCCAGGGCAAATGAAGGCTACACGAGCTGCGGCCCGGTAGTCGAGATGTCATGGCACAGGGCCGGTGTCCTGCTGCTAGGGGCTCAGTCCTGCCT[G/A]
CCTGTCCCGGGGGTTCCGGCCGTAGGTGGGATTGGGTCGGTACTCTTGTCTATGGCTAGGATGGGTTGGAAACTATGTCACGTCTTCCGTCTGTATACCG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 89.00% | 0.40% | 1.65% | 8.97% | NA |
| All Indica | 2759 | 91.80% | 0.50% | 2.36% | 5.33% | NA |
| All Japonica | 1512 | 81.30% | 0.20% | 0.66% | 17.86% | NA |
| Aus | 269 | 99.30% | 0.40% | 0.00% | 0.37% | NA |
| Indica I | 595 | 83.20% | 0.30% | 3.03% | 13.45% | NA |
| Indica II | 465 | 91.20% | 0.20% | 3.44% | 5.16% | NA |
| Indica III | 913 | 96.70% | 0.80% | 1.53% | 0.99% | NA |
| Indica Intermediate | 786 | 93.00% | 0.50% | 2.16% | 4.33% | NA |
| Temperate Japonica | 767 | 89.00% | 0.00% | 0.13% | 10.82% | NA |
| Tropical Japonica | 504 | 77.20% | 0.60% | 1.39% | 20.83% | NA |
| Japonica Intermediate | 241 | 65.10% | 0.00% | 0.83% | 34.02% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 90.00% | 1.10% | 3.33% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0101920381 | C -> T | LOC_Os01g04310.1 | synonymous_variant ; p.Leu17Leu; LOW | synonymous_codon | Average:6.858; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0101920381 | C -> DEL | LOC_Os01g04310.1 | N | frameshift_variant | Average:6.858; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |