| Variant ID: vg0322193886 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22193886 |
| 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: 74. )
TGGGGGCTCACTCCGGCGCCCCCGGGCCGTCGGCCTCGTCGCCGCTGTCGTCCGCACCGTCGTCACCGCCCTCCTCGTCGGAGTCGAGCGCGAACGCGAG[C/T]
CGAGGGGCCGTACCCTCGAAGCTGTGGACGATGTAGTCGGCGGCGTCCCGGACCCGCGCGCGCGCGCCATCCTCGGTTCCGGGAGGGAACTCTTCCAGCG
CGCTGGAAGAGTTCCCTCCCGGAACCGAGGATGGCGCGCGCGCGCGGGTCCGGGACGCCGCCGACTACATCGTCCACAGCTTCGAGGGTACGGCCCCTCG[G/A]
CTCGCGTTCGCGCTCGACTCCGACGAGGAGGGCGGTGACGACGGTGCGGACGACAGCGGCGACGAGGCCGACGGCCCGGGGGCGCCGGAGTGAGCCCCCA
| 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 | 9.70% | 1.90% | 30.72% | 57.64% | NA |
| All Indica | 2759 | 0.70% | 0.10% | 39.80% | 59.41% | NA |
| All Japonica | 1512 | 28.30% | 5.60% | 12.76% | 53.37% | NA |
| Aus | 269 | 0.40% | 0.00% | 46.84% | 52.79% | NA |
| Indica I | 595 | 0.50% | 0.00% | 21.18% | 78.32% | NA |
| Indica II | 465 | 1.10% | 0.00% | 25.38% | 73.55% | NA |
| Indica III | 913 | 0.50% | 0.00% | 66.48% | 32.97% | NA |
| Indica Intermediate | 786 | 0.80% | 0.40% | 31.42% | 67.43% | NA |
| Temperate Japonica | 767 | 19.30% | 0.00% | 15.51% | 65.19% | NA |
| Tropical Japonica | 504 | 41.70% | 16.30% | 9.13% | 32.94% | NA |
| Japonica Intermediate | 241 | 29.00% | 0.80% | 11.62% | 58.51% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 18.75% | 80.21% | NA |
| Intermediate | 90 | 12.20% | 3.30% | 18.89% | 65.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322193886 | C -> T | LOC_Os03g39930.1 | synonymous_variant ; p.Arg412Arg; LOW | synonymous_codon | Average:8.623; most accessible tissue: Zhenshan97 panicle, score: 28.447 | N | N | N | N |
| vg0322193886 | C -> DEL | LOC_Os03g39930.1 | N | frameshift_variant | Average:8.623; most accessible tissue: Zhenshan97 panicle, score: 28.447 | N | N | N | N |