| Variant ID: vg0400681161 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 681161 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 259. )
TAATAGGGGGATCCCAAGTAAAAAATTCTCAAATTAATACACTTTACTTCTTTTCCAACCACTGTTGAGTAACCACGTCTTTCGACGTATGCGGTTGTCG[T/A]
TTCGACAATACTATTATAAACTAAAAGTTCAGTACATTTCCTAAAAAACACTCGTACACCATCACATGATACCTTCTAAAATCAGAGAAATCCTCGAAAT
ATTTCGAGGATTTCTCTGATTTTAGAAGGTATCATGTGATGGTGTACGAGTGTTTTTTAGGAAATGTACTGAACTTTTAGTTTATAATAGTATTGTCGAA[A/T]
CGACAACCGCATACGTCGAAAGACGTGGTTACTCAACAGTGGTTGGAAAAGAAGTAAAGTGTATTAATTTGAGAATTTTTTACTTGGGATCCCCCTATTA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.40% | 6.90% | 2.01% | 0.78% | NA |
| All Indica | 2759 | 83.80% | 11.60% | 3.37% | 1.27% | NA |
| All Japonica | 1512 | 99.80% | 0.00% | 0.13% | 0.07% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 93.10% | 5.90% | 0.67% | 0.34% | NA |
| Indica II | 465 | 80.00% | 13.80% | 4.52% | 1.72% | NA |
| Indica III | 913 | 78.80% | 14.80% | 4.49% | 1.97% | NA |
| Indica Intermediate | 786 | 84.90% | 10.80% | 3.44% | 0.89% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 5.60% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0400681161 | T -> DEL | N | N | silent_mutation | Average:74.942; most accessible tissue: Minghui63 flag leaf, score: 85.67 | N | N | N | N |
| vg0400681161 | T -> A | LOC_Os04g02110.1 | 3_prime_UTR_variant ; 3130.0bp to feature; MODIFIER | silent_mutation | Average:74.942; most accessible tissue: Minghui63 flag leaf, score: 85.67 | N | N | N | N |
| vg0400681161 | T -> A | LOC_Os04g02110.3 | 3_prime_UTR_variant ; 3130.0bp to feature; MODIFIER | silent_mutation | Average:74.942; most accessible tissue: Minghui63 flag leaf, score: 85.67 | N | N | N | N |
| vg0400681161 | T -> A | LOC_Os04g02090.1 | upstream_gene_variant ; 4497.0bp to feature; MODIFIER | silent_mutation | Average:74.942; most accessible tissue: Minghui63 flag leaf, score: 85.67 | N | N | N | N |
| vg0400681161 | T -> A | LOC_Os04g02100.1 | downstream_gene_variant ; 173.0bp to feature; MODIFIER | silent_mutation | Average:74.942; most accessible tissue: Minghui63 flag leaf, score: 85.67 | N | N | N | N |
| vg0400681161 | T -> A | LOC_Os04g02110.2 | downstream_gene_variant ; 2544.0bp to feature; MODIFIER | silent_mutation | Average:74.942; most accessible tissue: Minghui63 flag leaf, score: 85.67 | N | N | N | N |