| Variant ID: vg0100791132 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 791132 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCATTATGAATTAGAGGTTCCTAACAAAGTTATAGAAAGTTGTTTTCCCTTATCTTTGTTATTACTAAACTTTGATGTAAACTATTTTTTTTTCTTCCTT[C/A]
CTTCAGGTTCACAAGTCATCCTCATTGCAGGTAATGCAGATATTCCCTGTTCTTCAAATTCTCGCCTGTCAGCAACCAAGATTTTGTGTACTCTTGTTCC
GGAACAAGAGTACACAAAATCTTGGTTGCTGACAGGCGAGAATTTGAAGAACAGGGAATATCTGCATTACCTGCAATGAGGATGACTTGTGAACCTGAAG[G/T]
AAGGAAGAAAAAAAAATAGTTTACATCAAAGTTTAGTAATAACAAAGATAAGGGAAAACAACTTTCTATAACTTTGTTAGGAACCTCTAATTCATAATGG
| 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 | 54.70% | 2.20% | 1.35% | 41.83% | NA |
| All Indica | 2759 | 49.70% | 0.80% | 1.96% | 47.52% | NA |
| All Japonica | 1512 | 73.70% | 0.00% | 0.20% | 26.06% | NA |
| Aus | 269 | 7.80% | 29.00% | 2.23% | 60.97% | NA |
| Indica I | 595 | 69.90% | 0.00% | 0.50% | 29.58% | NA |
| Indica II | 465 | 75.70% | 0.20% | 1.72% | 22.37% | NA |
| Indica III | 913 | 17.90% | 1.20% | 2.52% | 78.42% | NA |
| Indica Intermediate | 786 | 56.00% | 1.40% | 2.54% | 40.08% | NA |
| Temperate Japonica | 767 | 71.70% | 0.00% | 0.26% | 28.03% | NA |
| Tropical Japonica | 504 | 83.10% | 0.00% | 0.00% | 16.87% | NA |
| Japonica Intermediate | 241 | 60.60% | 0.00% | 0.41% | 39.00% | NA |
| VI/Aromatic | 96 | 11.50% | 1.00% | 0.00% | 87.50% | NA |
| Intermediate | 90 | 72.20% | 0.00% | 1.11% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100791132 | C -> A | LOC_Os01g02440.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:31.12; most accessible tissue: Callus, score: 47.641 | N | N | N | N |
| vg0100791132 | C -> A | LOC_Os01g02430.1 | upstream_gene_variant ; 2513.0bp to feature; MODIFIER | silent_mutation | Average:31.12; most accessible tissue: Callus, score: 47.641 | N | N | N | N |
| vg0100791132 | C -> A | LOC_Os01g02460.1 | upstream_gene_variant ; 3367.0bp to feature; MODIFIER | silent_mutation | Average:31.12; most accessible tissue: Callus, score: 47.641 | N | N | N | N |
| vg0100791132 | C -> A | LOC_Os01g02450.1 | downstream_gene_variant ; 1956.0bp to feature; MODIFIER | silent_mutation | Average:31.12; most accessible tissue: Callus, score: 47.641 | N | N | N | N |
| vg0100791132 | C -> DEL | N | N | silent_mutation | Average:31.12; most accessible tissue: Callus, score: 47.641 | N | N | N | N |