| Variant ID: vg0304212270 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 4212270 |
| Reference Allele: CACA | Alternative Allele: C,TACA,CAACA |
| Primary Allele: CACA | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TCGCAAAATTAACCGGCAAAATCACTGTGGGTGGTCTATTTCCACAGCATCTATCTCAAAATTGATATCTGGAATAACTTAATCTTAAACCTAAGACACA[CACA/C,TACA,CAACA]
AAAAAAAAACAACTTTTTCTTCATCATCAACACGCACAAAAACATAACACTAGTTATATACAGTGAAGCAAAGCTGCAGAGCAAACAAACCTGTGAGGCC
GGCCTCACAGGTTTGTTTGCTCTGCAGCTTTGCTTCACTGTATATAACTAGTGTTATGTTTTTGTGCGTGTTGATGATGAAGAAAAAGTTGTTTTTTTTT[TGTG/G,TGTA,TGTTG]
TGTGTCTTAGGTTTAAGATTAAGTTATTCCAGATATCAATTTTGAGATAGATGCTGTGGAAATAGACCACCCACAGTGATTTTGCCGGTTAATTTTGCGA
| Populations | Population Size | Frequency of CACA(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.20% | 1.90% | 0.36% | 0.28% | TACA: 0.19%; CAACA: 0.02% |
| All Indica | 2759 | 98.80% | 0.80% | 0.11% | 0.04% | TACA: 0.14%; CAACA: 0.04% |
| All Japonica | 1512 | 98.30% | 0.00% | 0.93% | 0.79% | NA |
| Aus | 269 | 75.50% | 23.80% | 0.00% | 0.00% | TACA: 0.74% |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.00% | 0.22% | NA |
| Indica III | 913 | 97.40% | 1.90% | 0.22% | 0.00% | TACA: 0.44%; CAACA: 0.11% |
| Indica Intermediate | 786 | 99.10% | 0.80% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.65% | 0.13% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.20% | 0.60% | NA |
| Japonica Intermediate | 241 | 93.40% | 0.00% | 3.32% | 3.32% | NA |
| VI/Aromatic | 96 | 93.80% | 3.10% | 0.00% | 0.00% | TACA: 3.12% |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0304212270 | CACA -> C | LOC_Os03g08270.1 | downstream_gene_variant ; 1966.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> C | LOC_Os03g08284.3 | downstream_gene_variant ; 4425.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> C | LOC_Os03g08270.2 | downstream_gene_variant ; 1966.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> C | LOC_Os03g08270.3 | downstream_gene_variant ; 1966.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> C | LOC_Os03g08270.5 | downstream_gene_variant ; 1966.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> C | LOC_Os03g08270.6 | downstream_gene_variant ; 1966.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> C | LOC_Os03g08284.1 | downstream_gene_variant ; 4425.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> C | LOC_Os03g08284.2 | downstream_gene_variant ; 4425.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> C | LOC_Os03g08280.1 | intron_variant ; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> C | LOC_Os03g08280.2 | intron_variant ; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> C | LOC_Os03g08280.3 | intron_variant ; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> DEL | N | N | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> CAACA | LOC_Os03g08270.1 | downstream_gene_variant ; 1967.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> CAACA | LOC_Os03g08284.3 | downstream_gene_variant ; 4424.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> CAACA | LOC_Os03g08270.2 | downstream_gene_variant ; 1967.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> CAACA | LOC_Os03g08270.3 | downstream_gene_variant ; 1967.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> CAACA | LOC_Os03g08270.5 | downstream_gene_variant ; 1967.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> CAACA | LOC_Os03g08270.6 | downstream_gene_variant ; 1967.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> CAACA | LOC_Os03g08284.1 | downstream_gene_variant ; 4424.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> CAACA | LOC_Os03g08284.2 | downstream_gene_variant ; 4424.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> CAACA | LOC_Os03g08280.1 | intron_variant ; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> CAACA | LOC_Os03g08280.2 | intron_variant ; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> CAACA | LOC_Os03g08280.3 | intron_variant ; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> TACA | LOC_Os03g08270.1 | downstream_gene_variant ; 1965.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> TACA | LOC_Os03g08284.3 | downstream_gene_variant ; 4426.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> TACA | LOC_Os03g08270.2 | downstream_gene_variant ; 1965.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> TACA | LOC_Os03g08270.3 | downstream_gene_variant ; 1965.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> TACA | LOC_Os03g08270.5 | downstream_gene_variant ; 1965.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> TACA | LOC_Os03g08270.6 | downstream_gene_variant ; 1965.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> TACA | LOC_Os03g08284.1 | downstream_gene_variant ; 4426.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> TACA | LOC_Os03g08284.2 | downstream_gene_variant ; 4426.0bp to feature; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> TACA | LOC_Os03g08280.1 | intron_variant ; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> TACA | LOC_Os03g08280.2 | intron_variant ; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212270 | CACA -> TACA | LOC_Os03g08280.3 | intron_variant ; MODIFIER | silent_mutation | Average:73.675; most accessible tissue: Callus, score: 91.123 | N | N | N | N |