| Variant ID: vg0202704838 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 2704838 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGAAGATCCTGCTGCAAGAACGGCCGCGCTCAGGATTATGTCTCTGCGGTGCCACAAGATAAACTGATTCACTGCATCACCGAGAAGTTCAATCCCCTCA[G/A]
GTGCAGGTATGTCTAGTTCCAAGGAAACGTGGTCGCTATGGACCTTGGCGACCTATACCCTTGCGTAATCCTCAGGGATTGCCGTGTTGTGGAATTGACG
CGTCAATTCCACAACACGGCAATCCCTGAGGATTACGCAAGGGTATAGGTCGCCAAGGTCCATAGCGACCACGTTTCCTTGGAACTAGACATACCTGCAC[C/T]
TGAGGGGATTGAACTTCTCGGTGATGCAGTGAATCAGTTTATCTTGTGGCACCGCAGAGACATAATCCTGAGCGCGGCCGTTCTTGCAGCAGGATCTTCA
| 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 | 27.70% | 0.10% | 4.27% | 67.94% | NA |
| All Indica | 2759 | 6.30% | 0.00% | 0.76% | 92.97% | NA |
| All Japonica | 1512 | 68.80% | 0.30% | 11.51% | 19.38% | NA |
| Aus | 269 | 17.80% | 0.00% | 0.37% | 81.78% | NA |
| Indica I | 595 | 11.10% | 0.00% | 0.34% | 88.57% | NA |
| Indica II | 465 | 1.90% | 0.00% | 0.86% | 97.20% | NA |
| Indica III | 913 | 6.50% | 0.00% | 0.66% | 92.88% | NA |
| Indica Intermediate | 786 | 5.00% | 0.00% | 1.15% | 93.89% | NA |
| Temperate Japonica | 767 | 52.30% | 0.00% | 17.08% | 30.64% | NA |
| Tropical Japonica | 504 | 93.80% | 0.40% | 3.57% | 2.18% | NA |
| Japonica Intermediate | 241 | 68.90% | 1.20% | 10.37% | 19.50% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 0.00% | 98.96% | NA |
| Intermediate | 90 | 51.10% | 0.00% | 6.67% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0202704838 | G -> A | LOC_Os02g05560.1 | downstream_gene_variant ; 4535.0bp to feature; MODIFIER | silent_mutation | Average:13.241; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg0202704838 | G -> A | LOC_Os02g05580.1 | downstream_gene_variant ; 3329.0bp to feature; MODIFIER | silent_mutation | Average:13.241; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg0202704838 | G -> A | LOC_Os02g05570.1 | intron_variant ; MODIFIER | silent_mutation | Average:13.241; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg0202704838 | G -> DEL | N | N | silent_mutation | Average:13.241; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |