| Variant ID: vg0335309927 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 35309927 |
| Reference Allele: CCTCAGTG | Alternative Allele: C |
| Primary Allele: CCTCAGTG | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AACTCTGGCAATTACGCAGTGTAGAGTTTGTAATTAAATGCATAATGCTCCAATTGTCTCTTTCCAACCTCCTTTCGAAACCGAAATGAAGGAAATGATG[CCTCAGTG/C]
CTCAGTGCTTACTTTAGTACTCTCTATTCTATGAATTTAGACACGTAAAGCACATATATACATCAAAACAGCCGAAATTCTGACAAATCGACCTTTAATA
TATTAAAGGTCGATTTGTCAGAATTTCGGCTGTTTTGATGTATATATGTGCTTTACGTGTCTAAATTCATAGAATAGAGAGTACTAAAGTAAGCACTGAG[CACTGAGG/G]
CATCATTTCCTTCATTTCGGTTTCGAAAGGAGGTTGGAAAGAGACAATTGGAGCATTATGCATTTAATTACAAACTCTACACTGCGTAATTGCCAGAGTT
| Populations | Population Size | Frequency of CCTCAGTG(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 95.10% | 4.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0335309927 | CCTCAGTG -> C | LOC_Os03g62330.1 | 3_prime_UTR_variant ; 375.0bp to feature; MODIFIER | silent_mutation | Average:66.892; most accessible tissue: Minghui63 root, score: 82.349 | N | N | N | N |
| vg0335309927 | CCTCAGTG -> C | LOC_Os03g62314.1 | upstream_gene_variant ; 542.0bp to feature; MODIFIER | silent_mutation | Average:66.892; most accessible tissue: Minghui63 root, score: 82.349 | N | N | N | N |
| vg0335309927 | CCTCAGTG -> C | LOC_Os03g62340.1 | downstream_gene_variant ; 2523.0bp to feature; MODIFIER | silent_mutation | Average:66.892; most accessible tissue: Minghui63 root, score: 82.349 | N | N | N | N |