| Variant ID: vg0202002803 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 2002803 |
| Reference Allele: AT | Alternative Allele: A,ATTT,ATT,TT |
| Primary Allele: AT | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCTAATTAATCCGTCATTAGCAAATGTTTACGGTAACATCACATTGTCAAATTATGGCGTAATTAGGCTCAAAAGATTCGTCTTGCAATTTATCTATGTT[AT/A,ATTT,ATT,TT]
TTTTTTTTTGAAACAGGCTCTGGTCAGAAGGAATGATCAAGAAGTGATCGACATGCTTCCAAGATCTGTGGACATTGTGGTTGGTGATGTTGGCGATGCT
AGCATCGCCAACATCACCAACCACAATGTCCACAGATCTTGGAAGCATGTCGATCACTTCTTGATCATTCCTTCTGACCAGAGCCTGTTTCAAAAAAAAA[AT/T,AAAT,AAT,AA]
AACATAGATAAATTGCAAGACGAATCTTTTGAGCCTAATTACGCCATAATTTGACAATGTGATGTTACCGTAAACATTTGCTAATGACGGATTAATTAGC
| 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 | 95.70% | 3.20% | 0.63% | 0.00% | ATT: 0.44%; TT: 0.04%; ATTT: 0.02% |
| All Indica | 2759 | 94.30% | 4.80% | 0.65% | 0.00% | ATT: 0.11%; TT: 0.07%; ATTT: 0.04% |
| All Japonica | 1512 | 98.40% | 0.00% | 0.66% | 0.00% | ATT: 0.93% |
| Aus | 269 | 93.70% | 5.60% | 0.74% | 0.00% | NA |
| Indica I | 595 | 98.00% | 0.30% | 1.34% | 0.00% | ATT: 0.34% |
| Indica II | 465 | 99.10% | 0.00% | 0.86% | 0.00% | NA |
| Indica III | 913 | 87.60% | 11.90% | 0.11% | 0.00% | TT: 0.22%; ATT: 0.11% |
| Indica Intermediate | 786 | 96.60% | 2.70% | 0.64% | 0.00% | ATTT: 0.13% |
| Temperate Japonica | 767 | 98.30% | 0.00% | 1.04% | 0.00% | ATT: 0.65% |
| Tropical Japonica | 504 | 98.20% | 0.00% | 0.40% | 0.00% | ATT: 1.39% |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.00% | ATT: 0.83% |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 0.00% | ATT: 4.17% |
| Intermediate | 90 | 95.60% | 4.40% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0202002803 | AT -> A | LOC_Os02g04520.1 | upstream_gene_variant ; 4428.0bp to feature; MODIFIER | silent_mutation | Average:71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 | N | N | N | N |
| vg0202002803 | AT -> A | LOC_Os02g04520.2 | upstream_gene_variant ; 4428.0bp to feature; MODIFIER | silent_mutation | Average:71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 | N | N | N | N |
| vg0202002803 | AT -> A | LOC_Os02g04500.1 | downstream_gene_variant ; 1883.0bp to feature; MODIFIER | silent_mutation | Average:71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 | N | N | N | N |
| vg0202002803 | AT -> A | LOC_Os02g04500.2 | downstream_gene_variant ; 1883.0bp to feature; MODIFIER | silent_mutation | Average:71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 | N | N | N | N |
| vg0202002803 | AT -> A | LOC_Os02g04510.1 | intron_variant ; MODIFIER | silent_mutation | Average:71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 | N | N | N | N |
| vg0202002803 | AT -> ATT | LOC_Os02g04520.1 | upstream_gene_variant ; 4427.0bp to feature; MODIFIER | silent_mutation | Average:71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 | N | N | N | N |
| vg0202002803 | AT -> ATT | LOC_Os02g04520.2 | upstream_gene_variant ; 4427.0bp to feature; MODIFIER | silent_mutation | Average:71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 | N | N | N | N |
| vg0202002803 | AT -> ATT | LOC_Os02g04500.1 | downstream_gene_variant ; 1884.0bp to feature; MODIFIER | silent_mutation | Average:71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 | N | N | N | N |
| vg0202002803 | AT -> ATT | LOC_Os02g04500.2 | downstream_gene_variant ; 1884.0bp to feature; MODIFIER | silent_mutation | Average:71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 | N | N | N | N |
| vg0202002803 | AT -> ATT | LOC_Os02g04510.1 | intron_variant ; MODIFIER | silent_mutation | Average:71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 | N | N | N | N |
| vg0202002803 | AT -> TT | LOC_Os02g04520.1 | upstream_gene_variant ; 4429.0bp to feature; MODIFIER | silent_mutation | Average:71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 | N | N | N | N |
| vg0202002803 | AT -> TT | LOC_Os02g04520.2 | upstream_gene_variant ; 4429.0bp to feature; MODIFIER | silent_mutation | Average:71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 | N | N | N | N |
| vg0202002803 | AT -> TT | LOC_Os02g04500.1 | downstream_gene_variant ; 1882.0bp to feature; MODIFIER | silent_mutation | Average:71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 | N | N | N | N |
| vg0202002803 | AT -> TT | LOC_Os02g04500.2 | downstream_gene_variant ; 1882.0bp to feature; MODIFIER | silent_mutation | Average:71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 | N | N | N | N |
| vg0202002803 | AT -> TT | LOC_Os02g04510.1 | intron_variant ; MODIFIER | silent_mutation | Average:71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 | N | N | N | N |
| vg0202002803 | AT -> ATTT | LOC_Os02g04520.1 | upstream_gene_variant ; 4427.0bp to feature; MODIFIER | silent_mutation | Average:71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 | N | N | N | N |
| vg0202002803 | AT -> ATTT | LOC_Os02g04520.2 | upstream_gene_variant ; 4427.0bp to feature; MODIFIER | silent_mutation | Average:71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 | N | N | N | N |
| vg0202002803 | AT -> ATTT | LOC_Os02g04500.1 | downstream_gene_variant ; 1884.0bp to feature; MODIFIER | silent_mutation | Average:71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 | N | N | N | N |
| vg0202002803 | AT -> ATTT | LOC_Os02g04500.2 | downstream_gene_variant ; 1884.0bp to feature; MODIFIER | silent_mutation | Average:71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 | N | N | N | N |
| vg0202002803 | AT -> ATTT | LOC_Os02g04510.1 | intron_variant ; MODIFIER | silent_mutation | Average:71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 | N | N | N | N |