| Variant ID: vg0722037535 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr07 | Position: 22037535 |
| Reference Allele: TCCC | Alternative Allele: ACCC,T |
| Primary Allele: TCCC | Secondary Allele: ACCC |
Inferred Ancestral Allele: Not determined.
CATCAGCACTGGCATCTCCATTCAACCTGGGGTCTAACAAGGTCTGCACATCACCTTCCTGGAGTTTGTTTACAGCCAAAGTTGGGAAGAAAGAGGACTT[TCCC/ACCC,T]
TCCTCCCCTAGATCAGCATTCCTTCTGCCTGATATGAGTTCGAAGAGCATCATGCCATAGCTGAAGACATCTGCCTTAGGAGTAATCGGCACACCACTGA
TCAGTGGTGTGCCGATTACTCCTAAGGCAGATGTCTTCAGCTATGGCATGATGCTCTTCGAACTCATATCAGGCAGAAGGAATGCTGATCTAGGGGAGGA[GGGA/GGGT,A]
AAGTCCTCTTTCTTCCCAACTTTGGCTGTAAACAAACTCCAGGAAGGTGATGTGCAGACCTTGTTAGACCCCAGGTTGAATGGAGATGCCAGTGCTGATG
| Populations | Population Size | Frequency of TCCC(primary allele) | Frequency of ACCC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.90% | 0.60% | 0.53% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 96.60% | 1.70% | 1.65% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 94.40% | 2.70% | 2.87% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 96.70% | 2.10% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0722037535 | TCCC -> ACCC | LOC_Os07g36780.1 | synonymous_variant ; p.Gly700Gly; LOW | synonymous_codon | Average:71.68; most accessible tissue: Callus, score: 88.307 | N | N | N | N |
| vg0722037535 | TCCC -> T | LOC_Os07g36780.1 | disruptive_inframe_deletion ; p.Gly700del; MODERATE | N | Average:71.68; most accessible tissue: Callus, score: 88.307 | N | N | N | N |
| vg0722037535 | TCCC -> T | LOC_Os07g36770.1 | upstream_gene_variant ; 2676.0bp to feature; MODIFIER | N | Average:71.68; most accessible tissue: Callus, score: 88.307 | N | N | N | N |