| Variant ID: vg0320571321 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 20571321 |
| Reference Allele: CAAAA | Alternative Allele: CAA,CA,C,CAAA |
| Primary Allele: CAAAA | Secondary Allele: CA |
Inferred Ancestral Allele: Not determined.
GACGCCTTCGAAGCAAAGGTGCGAACACAACTTGTTCCTCCTCAGCATTCCACACAGAATGACAAACTGACGACGATTGAATTTCTTGCCGATCGGTGAC[CAAAA/CAA,CA,C,CAAA]
AAAAAAAAAAAAAACAGGTCGCGGATTTCGGTCTTGCCAAATTCACCAACGATTCGGTGACTCATGTCTCGACGCGCGTGATGGGCACATTCGGGTAATT
AATTACCCGAATGTGCCCATCACGCGCGTCGAGACATGAGTCACCGAATCGTTGGTGAATTTGGCAAGACCGAAATCCGCGACCTGTTTTTTTTTTTTTT[TTTTG/TTG,TG,G,TTTG]
GTCACCGATCGGCAAGAAATTCAATCGTCGTCAGTTTGTCATTCTGTGTGGAATGCTGAGGAGGAACAAGTTGTGTTCGCACCTTTGCTTCGAAGGCGTC
| Populations | Population Size | Frequency of CAAAA(primary allele) | Frequency of CA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 55.60% | 11.80% | 30.11% | 0.36% | CAA: 1.93%; CAAA: 0.08%; C: 0.08% |
| All Indica | 2759 | 40.00% | 16.00% | 40.78% | 0.00% | CAA: 3.04%; C: 0.11%; CAAA: 0.04% |
| All Japonica | 1512 | 83.50% | 3.20% | 11.71% | 1.12% | CAAA: 0.20%; CAA: 0.20% |
| Aus | 269 | 45.40% | 18.60% | 34.94% | 0.00% | CAA: 0.74%; C: 0.37% |
| Indica I | 595 | 38.30% | 7.70% | 49.58% | 0.00% | CAA: 4.37% |
| Indica II | 465 | 34.60% | 19.40% | 45.16% | 0.00% | CAA: 0.86% |
| Indica III | 913 | 43.00% | 20.40% | 31.65% | 0.00% | CAA: 4.49%; C: 0.33%; CAAA: 0.11% |
| Indica Intermediate | 786 | 41.00% | 15.30% | 42.11% | 0.00% | CAA: 1.65% |
| Temperate Japonica | 767 | 89.60% | 0.00% | 9.00% | 1.30% | CAAA: 0.13% |
| Tropical Japonica | 504 | 73.80% | 8.90% | 16.87% | 0.20% | CAAA: 0.20% |
| Japonica Intermediate | 241 | 84.60% | 1.70% | 9.54% | 2.49% | CAA: 1.24%; CAAA: 0.41% |
| VI/Aromatic | 96 | 85.40% | 6.20% | 8.33% | 0.00% | NA |
| Intermediate | 90 | 65.60% | 11.10% | 21.11% | 0.00% | CAA: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0320571321 | CAAAA -> C | LOC_Os03g37110.1 | upstream_gene_variant ; 2799.0bp to feature; MODIFIER | silent_mutation | Average:66.579; most accessible tissue: Callus, score: 85.877 | N | N | N | N |
| vg0320571321 | CAAAA -> C | LOC_Os03g37130.1 | downstream_gene_variant ; 2919.0bp to feature; MODIFIER | silent_mutation | Average:66.579; most accessible tissue: Callus, score: 85.877 | N | N | N | N |
| vg0320571321 | CAAAA -> C | LOC_Os03g37120.1 | intron_variant ; MODIFIER | silent_mutation | Average:66.579; most accessible tissue: Callus, score: 85.877 | N | N | N | N |
| vg0320571321 | CAAAA -> CAA | LOC_Os03g37110.1 | upstream_gene_variant ; 2801.0bp to feature; MODIFIER | silent_mutation | Average:66.579; most accessible tissue: Callus, score: 85.877 | N | N | N | N |
| vg0320571321 | CAAAA -> CAA | LOC_Os03g37130.1 | downstream_gene_variant ; 2917.0bp to feature; MODIFIER | silent_mutation | Average:66.579; most accessible tissue: Callus, score: 85.877 | N | N | N | N |
| vg0320571321 | CAAAA -> CAA | LOC_Os03g37120.1 | intron_variant ; MODIFIER | silent_mutation | Average:66.579; most accessible tissue: Callus, score: 85.877 | N | N | N | N |
| vg0320571321 | CAAAA -> DEL | N | N | silent_mutation | Average:66.579; most accessible tissue: Callus, score: 85.877 | N | N | N | N |
| vg0320571321 | CAAAA -> CA | LOC_Os03g37110.1 | upstream_gene_variant ; 2800.0bp to feature; MODIFIER | silent_mutation | Average:66.579; most accessible tissue: Callus, score: 85.877 | N | N | N | N |
| vg0320571321 | CAAAA -> CA | LOC_Os03g37130.1 | downstream_gene_variant ; 2918.0bp to feature; MODIFIER | silent_mutation | Average:66.579; most accessible tissue: Callus, score: 85.877 | N | N | N | N |
| vg0320571321 | CAAAA -> CA | LOC_Os03g37120.1 | intron_variant ; MODIFIER | silent_mutation | Average:66.579; most accessible tissue: Callus, score: 85.877 | N | N | N | N |
| vg0320571321 | CAAAA -> CAAA | LOC_Os03g37110.1 | upstream_gene_variant ; 2802.0bp to feature; MODIFIER | silent_mutation | Average:66.579; most accessible tissue: Callus, score: 85.877 | N | N | N | N |
| vg0320571321 | CAAAA -> CAAA | LOC_Os03g37130.1 | downstream_gene_variant ; 2916.0bp to feature; MODIFIER | silent_mutation | Average:66.579; most accessible tissue: Callus, score: 85.877 | N | N | N | N |
| vg0320571321 | CAAAA -> CAAA | LOC_Os03g37120.1 | intron_variant ; MODIFIER | silent_mutation | Average:66.579; most accessible tissue: Callus, score: 85.877 | N | N | N | N |