| Variant ID: vg0400681164 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 681164 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.10, others allele: 0.00, population size: 200. )
TAGGGGGATCCCAAGTAAAAAATTCTCAAATTAATACACTTTACTTCTTTTCCAACCACTGTTGAGTAACCACGTCTTTCGACGTATGCGGTTGTCGTTT[C/T]
GACAATACTATTATAAACTAAAAGTTCAGTACATTTCCTAAAAAACACTCGTACACCATCACATGATACCTTCTAAAATCAGAGAAATCCTCGAAATTCT
AGAATTTCGAGGATTTCTCTGATTTTAGAAGGTATCATGTGATGGTGTACGAGTGTTTTTTAGGAAATGTACTGAACTTTTAGTTTATAATAGTATTGTC[G/A]
AAACGACAACCGCATACGTCGAAAGACGTGGTTACTCAACAGTGGTTGGAAAAGAAGTAAAGTGTATTAATTTGAGAATTTTTTACTTGGGATCCCCCTA
| 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 | 62.30% | 35.40% | 0.17% | 2.14% | NA |
| All Indica | 2759 | 70.90% | 26.20% | 0.18% | 2.79% | NA |
| All Japonica | 1512 | 42.20% | 56.30% | 0.00% | 1.46% | NA |
| Aus | 269 | 92.20% | 7.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 91.10% | 8.90% | 0.00% | 0.00% | NA |
| Indica II | 465 | 55.10% | 35.50% | 0.22% | 9.25% | NA |
| Indica III | 913 | 63.30% | 34.90% | 0.11% | 1.64% | NA |
| Indica Intermediate | 786 | 73.70% | 23.50% | 0.38% | 2.42% | NA |
| Temperate Japonica | 767 | 10.30% | 89.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 80.80% | 14.90% | 0.00% | 4.37% | NA |
| Japonica Intermediate | 241 | 63.10% | 36.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 46.90% | 53.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 63.30% | 31.10% | 3.33% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0400681164 | C -> DEL | N | N | silent_mutation | Average:75.167; most accessible tissue: Minghui63 flag leaf, score: 86.0 | N | N | N | N |
| vg0400681164 | C -> T | LOC_Os04g02110.1 | 3_prime_UTR_variant ; 3127.0bp to feature; MODIFIER | silent_mutation | Average:75.167; most accessible tissue: Minghui63 flag leaf, score: 86.0 | N | N | N | N |
| vg0400681164 | C -> T | LOC_Os04g02110.3 | 3_prime_UTR_variant ; 3127.0bp to feature; MODIFIER | silent_mutation | Average:75.167; most accessible tissue: Minghui63 flag leaf, score: 86.0 | N | N | N | N |
| vg0400681164 | C -> T | LOC_Os04g02090.1 | upstream_gene_variant ; 4500.0bp to feature; MODIFIER | silent_mutation | Average:75.167; most accessible tissue: Minghui63 flag leaf, score: 86.0 | N | N | N | N |
| vg0400681164 | C -> T | LOC_Os04g02100.1 | downstream_gene_variant ; 176.0bp to feature; MODIFIER | silent_mutation | Average:75.167; most accessible tissue: Minghui63 flag leaf, score: 86.0 | N | N | N | N |
| vg0400681164 | C -> T | LOC_Os04g02110.2 | downstream_gene_variant ; 2541.0bp to feature; MODIFIER | silent_mutation | Average:75.167; most accessible tissue: Minghui63 flag leaf, score: 86.0 | N | N | N | N |