| Variant ID: vg0620072673 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20072673 |
| 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: 390. )
ACACATTCTACACGAGAGCCCAAGACATGAAGAGCACGAACCAAAACAGCGCTGTTCGTGTCGATGCCATGGGACACGATGGAACAACTGCCACGTATTA[C/T]
GGTGCTATCGAGGACATATGGGAACTTGACTATGGTCCTCTCAAGGTTCCTCTGTTCCGGTGCCAATGGGTTAGGTTGACTGGTGGAGGCGTAATGATTG
CAATCATTACGCCTCCACCAGTCAACCTAACCCATTGGCACCGGAACAGAGGAACCTTGAGAGGACCATAGTCAAGTTCCCATATGTCCTCGATAGCACC[G/A]
TAATACGTGGCAGTTGTTCCATCGTGTCCCATGGCATCGACACGAACAGCGCTGTTTTGGTTCGTGCTCTTCATGTCTTGGGCTCTCGTGTAGAATGTGT
| 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 | 25.20% | 3.10% | 15.81% | 55.97% | NA |
| All Indica | 2759 | 7.60% | 0.00% | 15.44% | 76.95% | NA |
| All Japonica | 1512 | 61.80% | 9.50% | 6.15% | 22.49% | NA |
| Aus | 269 | 1.50% | 0.00% | 53.90% | 44.61% | NA |
| Indica I | 595 | 7.90% | 0.00% | 9.08% | 83.03% | NA |
| Indica II | 465 | 8.60% | 0.00% | 8.39% | 83.01% | NA |
| Indica III | 913 | 4.20% | 0.00% | 22.34% | 73.49% | NA |
| Indica Intermediate | 786 | 10.80% | 0.00% | 16.41% | 72.77% | NA |
| Temperate Japonica | 767 | 66.40% | 15.00% | 5.48% | 13.17% | NA |
| Tropical Japonica | 504 | 69.00% | 0.00% | 6.55% | 24.40% | NA |
| Japonica Intermediate | 241 | 32.40% | 12.00% | 7.47% | 48.13% | NA |
| VI/Aromatic | 96 | 1.00% | 1.00% | 66.67% | 31.25% | NA |
| Intermediate | 90 | 43.30% | 0.00% | 21.11% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620072673 | C -> T | LOC_Os06g34480.1 | synonymous_variant ; p.Tyr907Tyr; LOW | synonymous_codon | Average:6.581; most accessible tissue: Minghui63 young leaf, score: 13.864 | N | N | N | N |
| vg0620072673 | C -> DEL | LOC_Os06g34480.1 | N | frameshift_variant | Average:6.581; most accessible tissue: Minghui63 young leaf, score: 13.864 | N | N | N | N |