| Variant ID: vg0609018155 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9018155 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCTTTATAGTGTAACTCCTTTGTACTCCCTTGCATTTATTCTGCACTTGTGGGTGTGCCTTGTTGAGTACGGTGGTTGTACTCAGTCTTGCTCAATTTTT[T/C]
CCAAACCCAGAAGAGGAGTTCCAGGAGGATGAAGGCTTCGGTGTCTAGCTCGTGCCTGCCGTCAAGCGCCTGTGGTCGTCGCCCTAGTCTTCCGCTGTTT
AAACAGCGGAAGACTAGGGCGACGACCACAGGCGCTTGACGGCAGGCACGAGCTAGACACCGAAGCCTTCATCCTCCTGGAACTCCTCTTCTGGGTTTGG[A/G]
AAAAATTGAGCAAGACTGAGTACAACCACCGTACTCAACAAGGCACACCCACAAGTGCAGAATAAATGCAAGGGAGTACAAAGGAGTTACACTATAAAGG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.50% | 0.10% | 10.90% | 40.56% | NA |
| All Indica | 2759 | 58.80% | 0.10% | 7.79% | 33.35% | NA |
| All Japonica | 1512 | 40.60% | 0.00% | 10.91% | 48.48% | NA |
| Aus | 269 | 2.60% | 0.00% | 29.74% | 67.66% | NA |
| Indica I | 595 | 58.00% | 0.00% | 2.18% | 39.83% | NA |
| Indica II | 465 | 78.10% | 0.20% | 8.17% | 13.55% | NA |
| Indica III | 913 | 43.90% | 0.10% | 11.83% | 44.14% | NA |
| Indica Intermediate | 786 | 65.10% | 0.10% | 7.12% | 27.61% | NA |
| Temperate Japonica | 767 | 73.70% | 0.00% | 1.96% | 24.38% | NA |
| Tropical Japonica | 504 | 3.80% | 0.00% | 19.84% | 76.39% | NA |
| Japonica Intermediate | 241 | 12.40% | 0.00% | 20.75% | 66.80% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 40.62% | 55.21% | NA |
| Intermediate | 90 | 50.00% | 0.00% | 17.78% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609018155 | T -> C | LOC_Os06g15870.1 | upstream_gene_variant ; 3540.0bp to feature; MODIFIER | silent_mutation | Average:26.35; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 | N | N | N | N |
| vg0609018155 | T -> C | LOC_Os06g15900.1 | upstream_gene_variant ; 3259.0bp to feature; MODIFIER | silent_mutation | Average:26.35; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 | N | N | N | N |
| vg0609018155 | T -> C | LOC_Os06g15890.1 | downstream_gene_variant ; 1193.0bp to feature; MODIFIER | silent_mutation | Average:26.35; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 | N | N | N | N |
| vg0609018155 | T -> C | LOC_Os06g15880.1 | intron_variant ; MODIFIER | silent_mutation | Average:26.35; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 | N | N | N | N |
| vg0609018155 | T -> DEL | N | N | silent_mutation | Average:26.35; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 | N | N | N | N |