| Variant ID: vg1200353613 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 353613 |
| Reference Allele: CAAA | Alternative Allele: CA,CAA,CAAAA,C |
| Primary Allele: CA | Secondary Allele: CAA |
Inferred Ancestral Allele: Not determined.
TGATCTAAATGAACAGATGAAACTATTGATAAGCTCCAAGTCCATTTAGTACTTGCTCTATTAAACAAGTTTCATCTTGCTGCAATTTATCTCTATTAAA[CAAA/CA,CAA,CAAAA,C]
AAAAAAAACACTTTAACATACACCAATACATGATTCTCTAGGTGCGCTGCTAATTGCAAGAACCATAGCAGTAGTCCTGACATTCACTGTGTCGACATCC
GGATGTCGACACAGTGAATGTCAGGACTACTGCTATGGTTCTTGCAATTAGCAGCGCACCTAGAGAATCATGTATTGGTGTATGTTAAAGTGTTTTTTTT[TTTG/TG,TTG,TTTTG,G]
TTTAATAGAGATAAATTGCAGCAAGATGAAACTTGTTTAATAGAGCAAGTACTAAATGGACTTGGAGCTTATCAATAGTTTCATCTGTTCATTTAGATCA
| 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 | 63.70% | 18.30% | 1.21% | 0.00% | CAAA: 16.76%; CAAAA: 0.02%; C: 0.02% |
| All Indica | 2759 | 64.50% | 29.70% | 1.34% | 0.00% | CAAA: 4.46% |
| All Japonica | 1512 | 62.20% | 1.40% | 1.12% | 0.00% | CAAA: 35.19%; CAAAA: 0.07% |
| Aus | 269 | 50.60% | 6.70% | 0.74% | 0.00% | CAAA: 42.01% |
| Indica I | 595 | 51.10% | 45.50% | 1.68% | 0.00% | CAAA: 1.68% |
| Indica II | 465 | 91.00% | 8.20% | 0.43% | 0.00% | CAAA: 0.43% |
| Indica III | 913 | 62.40% | 30.10% | 1.53% | 0.00% | CAAA: 5.91% |
| Indica Intermediate | 786 | 61.50% | 29.90% | 1.40% | 0.00% | CAAA: 7.25% |
| Temperate Japonica | 767 | 39.40% | 1.80% | 1.69% | 0.00% | CAAA: 56.98%; CAAAA: 0.13% |
| Tropical Japonica | 504 | 93.50% | 1.40% | 0.79% | 0.00% | CAAA: 4.37% |
| Japonica Intermediate | 241 | 69.70% | 0.00% | 0.00% | 0.00% | CAAA: 30.29% |
| VI/Aromatic | 96 | 94.80% | 2.10% | 0.00% | 0.00% | CAAA: 3.12% |
| Intermediate | 90 | 71.10% | 3.30% | 1.11% | 0.00% | CAAA: 23.33%; C: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1200353613 | CAAA -> C | LOC_Os12g01574.1 | upstream_gene_variant ; 2969.0bp to feature; MODIFIER | silent_mutation | Average:57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg1200353613 | CAAA -> C | LOC_Os12g01570.1 | downstream_gene_variant ; 4469.0bp to feature; MODIFIER | silent_mutation | Average:57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg1200353613 | CAAA -> C | LOC_Os12g01590.1 | downstream_gene_variant ; 1909.0bp to feature; MODIFIER | silent_mutation | Average:57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg1200353613 | CAAA -> C | LOC_Os12g01580.1 | intron_variant ; MODIFIER | silent_mutation | Average:57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg1200353613 | CAAA -> C | LOC_Os12g01580.2 | intron_variant ; MODIFIER | silent_mutation | Average:57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg1200353613 | CAAA -> CA | LOC_Os12g01574.1 | upstream_gene_variant ; 2970.0bp to feature; MODIFIER | silent_mutation | Average:57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg1200353613 | CAAA -> CA | LOC_Os12g01570.1 | downstream_gene_variant ; 4470.0bp to feature; MODIFIER | silent_mutation | Average:57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg1200353613 | CAAA -> CA | LOC_Os12g01590.1 | downstream_gene_variant ; 1908.0bp to feature; MODIFIER | silent_mutation | Average:57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg1200353613 | CAAA -> CA | LOC_Os12g01580.1 | intron_variant ; MODIFIER | silent_mutation | Average:57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg1200353613 | CAAA -> CA | LOC_Os12g01580.2 | intron_variant ; MODIFIER | silent_mutation | Average:57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg1200353613 | CAAA -> CAAAA | LOC_Os12g01574.1 | upstream_gene_variant ; 2972.0bp to feature; MODIFIER | silent_mutation | Average:57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg1200353613 | CAAA -> CAAAA | LOC_Os12g01570.1 | downstream_gene_variant ; 4472.0bp to feature; MODIFIER | silent_mutation | Average:57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg1200353613 | CAAA -> CAAAA | LOC_Os12g01590.1 | downstream_gene_variant ; 1906.0bp to feature; MODIFIER | silent_mutation | Average:57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg1200353613 | CAAA -> CAAAA | LOC_Os12g01580.1 | intron_variant ; MODIFIER | silent_mutation | Average:57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg1200353613 | CAAA -> CAAAA | LOC_Os12g01580.2 | intron_variant ; MODIFIER | silent_mutation | Average:57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg1200353613 | CAAA -> CAA | LOC_Os12g01574.1 | upstream_gene_variant ; 2971.0bp to feature; MODIFIER | silent_mutation | Average:57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg1200353613 | CAAA -> CAA | LOC_Os12g01570.1 | downstream_gene_variant ; 4471.0bp to feature; MODIFIER | silent_mutation | Average:57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg1200353613 | CAAA -> CAA | LOC_Os12g01590.1 | downstream_gene_variant ; 1907.0bp to feature; MODIFIER | silent_mutation | Average:57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg1200353613 | CAAA -> CAA | LOC_Os12g01580.1 | intron_variant ; MODIFIER | silent_mutation | Average:57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg1200353613 | CAAA -> CAA | LOC_Os12g01580.2 | intron_variant ; MODIFIER | silent_mutation | Average:57.127; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |