| Variant ID: vg0202539910 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 2539910 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGATCCCCGTACCATGCAAATACCGGAATCGCGACATCAAACGTCGACAATGGCGCGCTAGGTAGGGGGAGTTTGGTACTTCAAGGTTTCGACGAGATGG[G/A]
TTCAAAAGATGGATTCTCTGACAACAAGCTATTCGACGACTTCGCTGTGGGAAGATCCAACCCGACCGAAGTATGTCTCCCGACGAGATCGGAACCATCG
CGATGGTTCCGATCTCGTCGGGAGACATACTTCGGTCGGGTTGGATCTTCCCACAGCGAAGTCGTCGAATAGCTTGTTGTCAGAGAATCCATCTTTTGAA[C/T]
CCATCTCGTCGAAACCTTGAAGTACCAAACTCCCCCTACCTAGCGCGCCATTGTCGACGTTTGATGTCGCGATTCCGGTATTTGCATGGTACGGGGATCG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0202539910 | G -> A | LOC_Os02g05290.1 | missense_variant ; p.Gly2Asp; MODERATE | N | Average:47.286; most accessible tissue: Minghui63 young leaf, score: 65.92 | N | N | N | N |
| vg0202539910 | G -> A | LOC_Os02g05270.1 | upstream_gene_variant ; 3735.0bp to feature; MODIFIER | N | Average:47.286; most accessible tissue: Minghui63 young leaf, score: 65.92 | N | N | N | N |
| vg0202539910 | G -> A | LOC_Os02g05280.1 | downstream_gene_variant ; 1240.0bp to feature; MODIFIER | N | Average:47.286; most accessible tissue: Minghui63 young leaf, score: 65.92 | N | N | N | N |
| vg0202539910 | G -> A | LOC_Os02g05300.1 | downstream_gene_variant ; 2180.0bp to feature; MODIFIER | N | Average:47.286; most accessible tissue: Minghui63 young leaf, score: 65.92 | N | N | N | N |