| Variant ID: vg1100674296 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 674296 |
| Reference Allele: CAA | Alternative Allele: C |
| Primary Allele: CAA | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GAAATGTGCCTGTTCCACTGAGAGTCCTCGTTTTTGAGTATGTCACAATCATTGTGGTTAGGACTTTGGAGAAGTGCATTGTTTCCCAACATGCATCAGA[CAA/C]
AATGAAAATATTGGGTTTCTATCCATTTCCATTGCAATATGTGAAATTTTGGATGTCTACTCCACTGAATGTCTGTTGTCAGTAAACTGCACTGGCTAAA
TTTAGCCAGTGCAGTTTACTGACAACAGACATTCAGTGGAGTAGACATCCAAAATTTCACATATTGCAATGGAAATGGATAGAAACCCAATATTTTCATT[TTG/G]
TCTGATGCATGTTGGGAAACAATGCACTTCTCCAAAGTCCTAACCACAATGATTGTGACATACTCAAAAACGAGGACTCTCAGTGGAACAGGCACATTTC
| Populations | Population Size | Frequency of CAA(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 73.10% | 10.20% | 16.27% | 0.40% | NA |
| All Indica | 2759 | 60.50% | 14.20% | 24.65% | 0.65% | NA |
| All Japonica | 1512 | 99.80% | 0.10% | 0.07% | 0.00% | NA |
| Aus | 269 | 40.50% | 28.30% | 30.86% | 0.37% | NA |
| Indica I | 595 | 66.40% | 24.50% | 9.08% | 0.00% | NA |
| Indica II | 465 | 76.80% | 4.50% | 18.06% | 0.65% | NA |
| Indica III | 913 | 48.50% | 10.40% | 40.31% | 0.77% | NA |
| Indica Intermediate | 786 | 60.40% | 16.40% | 22.14% | 1.02% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.40% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 92.70% | 5.20% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 7.80% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1100674296 | CAA -> DEL | N | N | silent_mutation | Average:49.756; most accessible tissue: Minghui63 flower, score: 65.9 | N | N | N | N |
| vg1100674296 | CAA -> C | LOC_Os11g02310.1 | 3_prime_UTR_variant ; 1091.0bp to feature; MODIFIER | silent_mutation | Average:49.756; most accessible tissue: Minghui63 flower, score: 65.9 | N | N | N | N |
| vg1100674296 | CAA -> C | LOC_Os11g02320.1 | upstream_gene_variant ; 2596.0bp to feature; MODIFIER | silent_mutation | Average:49.756; most accessible tissue: Minghui63 flower, score: 65.9 | N | N | N | N |
| vg1100674296 | CAA -> C | LOC_Os11g02320.2 | upstream_gene_variant ; 2596.0bp to feature; MODIFIER | silent_mutation | Average:49.756; most accessible tissue: Minghui63 flower, score: 65.9 | N | N | N | N |
| vg1100674296 | CAA -> C | LOC_Os11g02320.3 | upstream_gene_variant ; 2596.0bp to feature; MODIFIER | silent_mutation | Average:49.756; most accessible tissue: Minghui63 flower, score: 65.9 | N | N | N | N |