| Variant ID: vg0304212272 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 4212272 |
| Reference Allele: CA | Alternative Allele: CAA,C,CAAA,CAAAA |
| Primary Allele: CA | Secondary Allele: CAA |
Inferred Ancestral Allele: Not determined.
GCAAAATTAACCGGCAAAATCACTGTGGGTGGTCTATTTCCACAGCATCTATCTCAAAATTGATATCTGGAATAACTTAATCTTAAACCTAAGACACACA[CA/CAA,C,CAAA,CAAAA]
AAAAAAAAACAACTTTTTCTTCATCATCAACACGCACAAAAACATAACACTAGTTATATACAGTGAAGCAAAGCTGCAGAGCAAACAAACCTGTGAGGCC
GGCCTCACAGGTTTGTTTGCTCTGCAGCTTTGCTTCACTGTATATAACTAGTGTTATGTTTTTGTGCGTGTTGATGATGAAGAAAAAGTTGTTTTTTTTT[TG/TTG,G,TTTG,TTTTG]
TGTGTGTCTTAGGTTTAAGATTAAGTTATTCCAGATATCAATTTTGAGATAGATGCTGTGGAAATAGACCACCCACAGTGATTTTGCCGGTTAATTTTGC
| Populations | Population Size | Frequency of CA(primary allele) | Frequency of CAA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 68.50% | 28.40% | 2.58% | 0.00% | C: 0.32%; CAAA: 0.19%; CAAAA: 0.04% |
| All Indica | 2759 | 72.30% | 24.90% | 2.39% | 0.00% | C: 0.36% |
| All Japonica | 1512 | 54.80% | 41.00% | 3.31% | 0.00% | CAAA: 0.53%; C: 0.20%; CAAAA: 0.13% |
| Aus | 269 | 97.00% | 1.50% | 1.12% | 0.00% | C: 0.37% |
| Indica I | 595 | 85.90% | 11.90% | 2.18% | 0.00% | NA |
| Indica II | 465 | 64.70% | 34.00% | 1.29% | 0.00% | NA |
| Indica III | 913 | 71.30% | 26.50% | 1.42% | 0.00% | C: 0.77% |
| Indica Intermediate | 786 | 67.80% | 27.50% | 4.33% | 0.00% | C: 0.38% |
| Temperate Japonica | 767 | 87.40% | 9.40% | 3.00% | 0.00% | C: 0.26% |
| Tropical Japonica | 504 | 13.10% | 83.10% | 1.79% | 0.00% | CAAA: 1.59%; CAAAA: 0.40% |
| Japonica Intermediate | 241 | 38.60% | 53.50% | 7.47% | 0.00% | C: 0.41% |
| VI/Aromatic | 96 | 95.80% | 3.10% | 0.00% | 0.00% | C: 1.04% |
| Intermediate | 90 | 66.70% | 28.90% | 3.33% | 0.00% | CAAA: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0304212272 | CA -> C | LOC_Os03g08270.1 | downstream_gene_variant ; 1968.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> C | LOC_Os03g08284.3 | downstream_gene_variant ; 4423.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> C | LOC_Os03g08270.2 | downstream_gene_variant ; 1968.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> C | LOC_Os03g08270.3 | downstream_gene_variant ; 1968.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> C | LOC_Os03g08270.5 | downstream_gene_variant ; 1968.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> C | LOC_Os03g08270.6 | downstream_gene_variant ; 1968.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> C | LOC_Os03g08284.1 | downstream_gene_variant ; 4423.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> C | LOC_Os03g08284.2 | downstream_gene_variant ; 4423.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> C | LOC_Os03g08280.1 | intron_variant ; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> C | LOC_Os03g08280.2 | intron_variant ; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> C | LOC_Os03g08280.3 | intron_variant ; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAA | LOC_Os03g08270.1 | downstream_gene_variant ; 1969.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAA | LOC_Os03g08284.3 | downstream_gene_variant ; 4422.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAA | LOC_Os03g08270.2 | downstream_gene_variant ; 1969.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAA | LOC_Os03g08270.3 | downstream_gene_variant ; 1969.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAA | LOC_Os03g08270.5 | downstream_gene_variant ; 1969.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAA | LOC_Os03g08270.6 | downstream_gene_variant ; 1969.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAA | LOC_Os03g08284.1 | downstream_gene_variant ; 4422.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAA | LOC_Os03g08284.2 | downstream_gene_variant ; 4422.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAA | LOC_Os03g08280.1 | intron_variant ; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAA | LOC_Os03g08280.2 | intron_variant ; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAA | LOC_Os03g08280.3 | intron_variant ; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAA | LOC_Os03g08270.1 | downstream_gene_variant ; 1969.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAA | LOC_Os03g08284.3 | downstream_gene_variant ; 4422.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAA | LOC_Os03g08270.2 | downstream_gene_variant ; 1969.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAA | LOC_Os03g08270.3 | downstream_gene_variant ; 1969.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAA | LOC_Os03g08270.5 | downstream_gene_variant ; 1969.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAA | LOC_Os03g08270.6 | downstream_gene_variant ; 1969.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAA | LOC_Os03g08284.1 | downstream_gene_variant ; 4422.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAA | LOC_Os03g08284.2 | downstream_gene_variant ; 4422.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAA | LOC_Os03g08280.1 | intron_variant ; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAA | LOC_Os03g08280.2 | intron_variant ; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAA | LOC_Os03g08280.3 | intron_variant ; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAAA | LOC_Os03g08270.1 | downstream_gene_variant ; 1969.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAAA | LOC_Os03g08284.3 | downstream_gene_variant ; 4422.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAAA | LOC_Os03g08270.2 | downstream_gene_variant ; 1969.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAAA | LOC_Os03g08270.3 | downstream_gene_variant ; 1969.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAAA | LOC_Os03g08270.5 | downstream_gene_variant ; 1969.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAAA | LOC_Os03g08270.6 | downstream_gene_variant ; 1969.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAAA | LOC_Os03g08284.1 | downstream_gene_variant ; 4422.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAAA | LOC_Os03g08284.2 | downstream_gene_variant ; 4422.0bp to feature; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAAA | LOC_Os03g08280.1 | intron_variant ; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAAA | LOC_Os03g08280.2 | intron_variant ; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212272 | CA -> CAAAA | LOC_Os03g08280.3 | intron_variant ; MODIFIER | silent_mutation | Average:73.671; most accessible tissue: Callus, score: 91.123 | N | N | N | N |