| Variant ID: vg0101920363 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 1920363 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 386. )
ACGTGCCACATACCACCACGGTATACAGACGGAAGACGTGACATAGTTTCCAACCCATCCTAGCCATAGACAAGAGTACCGACCCAATCCCACCTACGGC[C/T]
GGAACCCCCGGGACAGGCAGGCAGGACTGAGCCCCTAGCAGCAGGACACCGGCCCTGTGCCATGACATCTCGACTACCGGGCCGCAGCTCGTGTAGCCTT
AAGGCTACACGAGCTGCGGCCCGGTAGTCGAGATGTCATGGCACAGGGCCGGTGTCCTGCTGCTAGGGGCTCAGTCCTGCCTGCCTGTCCCGGGGGTTCC[G/A]
GCCGTAGGTGGGATTGGGTCGGTACTCTTGTCTATGGCTAGGATGGGTTGGAAACTATGTCACGTCTTCCGTCTGTATACCGTGGTGGTATGTGGCACGT
| 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 | 89.20% | 0.10% | 1.71% | 9.04% | NA |
| All Indica | 2759 | 91.80% | 0.10% | 2.25% | 5.80% | NA |
| All Japonica | 1512 | 81.70% | 0.00% | 1.06% | 17.20% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.37% | NA |
| Indica I | 595 | 83.50% | 0.00% | 3.03% | 13.45% | NA |
| Indica II | 465 | 91.20% | 0.00% | 3.01% | 5.81% | NA |
| Indica III | 913 | 96.80% | 0.30% | 1.10% | 1.75% | NA |
| Indica Intermediate | 786 | 92.70% | 0.00% | 2.54% | 4.71% | NA |
| Temperate Japonica | 767 | 89.00% | 0.00% | 0.13% | 10.82% | NA |
| Tropical Japonica | 504 | 78.40% | 0.00% | 1.98% | 19.64% | NA |
| Japonica Intermediate | 241 | 65.60% | 0.00% | 2.07% | 32.37% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0101920363 | C -> T | LOC_Os01g04310.1 | synonymous_variant ; p.Pro23Pro; LOW | synonymous_codon | Average:7.146; most accessible tissue: Zhenshan97 flag leaf, score: 11.736 | N | N | N | N |
| vg0101920363 | C -> DEL | LOC_Os01g04310.1 | N | frameshift_variant | Average:7.146; most accessible tissue: Zhenshan97 flag leaf, score: 11.736 | N | N | N | N |