| Variant ID: vg0202004000 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 2004000 |
| Reference Allele: C | Alternative Allele: A,CA |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.92, C: 0.07, others allele: 0.00, population size: 277. )
TTCAGGTGAGAGTGCCGTTCTCAGATTTCAGGCCAGTGAACCCACAGGACCCTCCTCTTGACCCTTTTCTTGTGCACACATTAACCATAAGGTTTGAACC[C/A,CA]
AAAAAACAGGTCAGTGCAAAATGATTTGTTGAATCAATTGGAGATAGGCAATGCTTCTGGAAGTTGTTAGTTTACCAATAAAATCCTTGTGCAGAGACCT
AGGTCTCTGCACAAGGATTTTATTGGTAAACTAACAACTTCCAGAAGCATTGCCTATCTCCAATTGATTCAACAAATCATTTTGCACTGACCTGTTTTTT[G/T,TG]
GGTTCAAACCTTATGGTTAATGTGTGCACAAGAAAAGGGTCAAGAGGAGGGTCCTGTGGGTTCACTGGCCTGAAATCTGAGAACGGCACTCTCACCTGAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.60% | 3.40% | 0.02% | 0.00% | CA: 0.02% |
| All Indica | 2759 | 95.10% | 4.90% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.20% | 0.00% | 0.00% | CA: 0.07% |
| Aus | 269 | 92.90% | 7.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 87.70% | 12.20% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.40% | 0.00% | 0.00% | CA: 0.20% |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 4.40% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0202004000 | C -> A | LOC_Os02g04510.1 | synonymous_variant ; p.Pro433Pro; LOW | synonymous_codon | Average:66.659; most accessible tissue: Minghui63 flag leaf, score: 86.911 | N | N | N | N |
| vg0202004000 | C -> CA | LOC_Os02g04510.1 | frameshift_variant&splice_region_variant ; p.Gln436fs; HIGH | frameshift_variant | Average:66.659; most accessible tissue: Minghui63 flag leaf, score: 86.911 | N | N | N | N |