| Variant ID: vg0400681177 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 681177 |
| Reference Allele: AT | Alternative Allele: A |
| Primary Allele: AT | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AGTAAAAAATTCTCAAATTAATACACTTTACTTCTTTTCCAACCACTGTTGAGTAACCACGTCTTTCGACGTATGCGGTTGTCGTTTCGACAATACTATT[AT/A]
AAACTAAAAGTTCAGTACATTTCCTAAAAAACACTCGTACACCATCACATGATACCTTCTAAAATCAGAGAAATCCTCGAAATTCTAAAAAAAAAATCTG
CAGATTTTTTTTTTAGAATTTCGAGGATTTCTCTGATTTTAGAAGGTATCATGTGATGGTGTACGAGTGTTTTTTAGGAAATGTACTGAACTTTTAGTTT[AT/T]
AATAGTATTGTCGAAACGACAACCGCATACGTCGAAAGACGTGGTTACTCAACAGTGGTTGGAAAAGAAGTAAAGTGTATTAATTTGAGAATTTTTTACT
| Populations | Population Size | Frequency of AT(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.30% | 0.00% | 0.34% | 1.31% | NA |
| All Indica | 2759 | 97.80% | 0.00% | 0.36% | 1.78% | NA |
| All Japonica | 1512 | 98.80% | 0.00% | 0.40% | 0.79% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 92.50% | 0.20% | 0.22% | 7.10% | NA |
| Indica III | 913 | 99.10% | 0.00% | 0.77% | 0.11% | NA |
| Indica Intermediate | 786 | 97.80% | 0.00% | 0.25% | 1.91% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 96.40% | 0.00% | 1.19% | 2.38% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0400681177 | AT -> DEL | N | N | silent_mutation | Average:78.583; most accessible tissue: Minghui63 flag leaf, score: 86.911 | N | N | N | N |
| vg0400681177 | AT -> A | LOC_Os04g02110.1 | 3_prime_UTR_variant ; 3113.0bp to feature; MODIFIER | silent_mutation | Average:78.583; most accessible tissue: Minghui63 flag leaf, score: 86.911 | N | N | N | N |
| vg0400681177 | AT -> A | LOC_Os04g02110.3 | 3_prime_UTR_variant ; 3113.0bp to feature; MODIFIER | silent_mutation | Average:78.583; most accessible tissue: Minghui63 flag leaf, score: 86.911 | N | N | N | N |
| vg0400681177 | AT -> A | LOC_Os04g02090.1 | upstream_gene_variant ; 4514.0bp to feature; MODIFIER | silent_mutation | Average:78.583; most accessible tissue: Minghui63 flag leaf, score: 86.911 | N | N | N | N |
| vg0400681177 | AT -> A | LOC_Os04g02100.1 | downstream_gene_variant ; 190.0bp to feature; MODIFIER | silent_mutation | Average:78.583; most accessible tissue: Minghui63 flag leaf, score: 86.911 | N | N | N | N |
| vg0400681177 | AT -> A | LOC_Os04g02110.2 | downstream_gene_variant ; 2527.0bp to feature; MODIFIER | silent_mutation | Average:78.583; most accessible tissue: Minghui63 flag leaf, score: 86.911 | N | N | N | N |