| Variant ID: vg0400681200 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 681200 |
| Reference Allele: TCCTAAAAAACAC | Alternative Allele: T |
| Primary Allele: TCCTAAAAAACAC | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CACTTTACTTCTTTTCCAACCACTGTTGAGTAACCACGTCTTTCGACGTATGCGGTTGTCGTTTCGACAATACTATTATAAACTAAAAGTTCAGTACATT[TCCTAAAAAACAC/T]
TCGTACACCATCACATGATACCTTCTAAAATCAGAGAAATCCTCGAAATTCTAAAAAAAAAATCTGACCATCAACTATCATTTAAACCGACCGGTCCACC
GGTGGACCGGTCGGTTTAAATGATAGTTGATGGTCAGATTTTTTTTTTAGAATTTCGAGGATTTCTCTGATTTTAGAAGGTATCATGTGATGGTGTACGA[GTGTTTTTTAGGA/A]
AATGTACTGAACTTTTAGTTTATAATAGTATTGTCGAAACGACAACCGCATACGTCGAAAGACGTGGTTACTCAACAGTGGTTGGAAAAGAAGTAAAGTG
| Populations | Population Size | Frequency of TCCTAAAAAACAC(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.10% | 0.10% | 1.46% | 2.31% | NA |
| All Indica | 2759 | 94.10% | 0.30% | 1.81% | 3.88% | NA |
| All Japonica | 1512 | 98.80% | 0.00% | 1.12% | 0.07% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.50% | 0.00% | 0.17% | 1.34% | NA |
| Indica II | 465 | 91.80% | 0.00% | 0.65% | 7.53% | NA |
| Indica III | 913 | 91.80% | 0.80% | 4.05% | 3.40% | NA |
| Indica Intermediate | 786 | 94.70% | 0.00% | 1.15% | 4.20% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 96.40% | 0.00% | 3.37% | 0.20% | 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 | 96.70% | 0.00% | 2.22% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0400681200 | TCCTAAAAAACAC -> DEL | N | N | silent_mutation | Average:79.095; most accessible tissue: Minghui63 flag leaf, score: 87.326 | N | N | N | N |
| vg0400681200 | TCCTAAAAAACAC -> T | LOC_Os04g02110.1 | 3_prime_UTR_variant ; 3079.0bp to feature; MODIFIER | silent_mutation | Average:79.095; most accessible tissue: Minghui63 flag leaf, score: 87.326 | N | N | N | N |
| vg0400681200 | TCCTAAAAAACAC -> T | LOC_Os04g02110.3 | 3_prime_UTR_variant ; 3079.0bp to feature; MODIFIER | silent_mutation | Average:79.095; most accessible tissue: Minghui63 flag leaf, score: 87.326 | N | N | N | N |
| vg0400681200 | TCCTAAAAAACAC -> T | LOC_Os04g02090.1 | upstream_gene_variant ; 4537.0bp to feature; MODIFIER | silent_mutation | Average:79.095; most accessible tissue: Minghui63 flag leaf, score: 87.326 | N | N | N | N |
| vg0400681200 | TCCTAAAAAACAC -> T | LOC_Os04g02100.1 | downstream_gene_variant ; 213.0bp to feature; MODIFIER | silent_mutation | Average:79.095; most accessible tissue: Minghui63 flag leaf, score: 87.326 | N | N | N | N |
| vg0400681200 | TCCTAAAAAACAC -> T | LOC_Os04g02110.2 | downstream_gene_variant ; 2504.0bp to feature; MODIFIER | silent_mutation | Average:79.095; most accessible tissue: Minghui63 flag leaf, score: 87.326 | N | N | N | N |