| Variant ID: vg0318608236 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 18608236 |
| Reference Allele: AACACACACAC | Alternative Allele: AAC,AACACAC,AACACACAC,AACAC,A |
| Primary Allele: AACACACACAC | Secondary Allele: AAC |
Inferred Ancestral Allele: Not determined.
ACCTTGTGGAACCCCTCCGACTCGGTGCACGACGCCACAATCCCCTTCTGCCAGTTCTGCCCAGCCTCTGCCCACACAGAAACGCAAGGGAGAGAAAAAC[AACACACACAC/AAC,AACACAC,AACACACAC,AACAC,A]
ACACACACACACTGTTAAATAAACCGACAGCAAATTGGGGGGGCAACACGAAATCGGGCGCGCCACCCACCCACCCACCTTCCTCCTCGTCGCTGCGCCC
GGGCGCAGCGACGAGGAGGAAGGTGGGTGGGTGGGTGGCGCGCCCGATTTCGTGTTGCCCCCCCAATTTGCTGTCGGTTTATTTAACAGTGTGTGTGTGT[GTGTGTGTGTT/GTT,GTGTGTT,GTGTGTGTT,GTGTT,T]
GTTTTTCTCTCCCTTGCGTTTCTGTGTGGGCAGAGGCTGGGCAGAACTGGCAGAAGGGGATTGTGGCGTCGTGCACCGAGTCGGAGGGGTTCCACAAGGT
| Populations | Population Size | Frequency of AACACACACAC(primary allele) | Frequency of AAC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.70% | 9.60% | 32.65% | 0.08% | AACACAC: 3.13%; AACACACAC: 2.56%; AACAC: 0.25%; A: 0.04% |
| All Indica | 2759 | 42.30% | 12.70% | 41.17% | 0.00% | AACACAC: 3.44%; AACAC: 0.29%; AACACACAC: 0.14% |
| All Japonica | 1512 | 71.70% | 0.00% | 17.79% | 0.26% | AACACACAC: 7.08%; AACACAC: 3.04%; AACAC: 0.13% |
| Aus | 269 | 21.20% | 38.70% | 36.80% | 0.00% | AACACAC: 1.86%; A: 0.74%; AACAC: 0.37%; AACACACAC: 0.37% |
| Indica I | 595 | 23.50% | 5.50% | 64.71% | 0.00% | AACACAC: 6.22% |
| Indica II | 465 | 28.60% | 28.60% | 40.65% | 0.00% | AACACAC: 2.15% |
| Indica III | 913 | 62.20% | 8.50% | 25.41% | 0.00% | AACACAC: 2.85%; AACAC: 0.77%; AACACACAC: 0.22% |
| Indica Intermediate | 786 | 41.30% | 13.50% | 41.98% | 0.00% | AACACAC: 2.80%; AACACACAC: 0.25%; AACAC: 0.13% |
| Temperate Japonica | 767 | 94.80% | 0.00% | 1.30% | 0.00% | AACACACAC: 2.35%; AACACAC: 1.56% |
| Tropical Japonica | 504 | 41.90% | 0.00% | 40.87% | 0.79% | AACACACAC: 10.91%; AACACAC: 5.16%; AACAC: 0.40% |
| Japonica Intermediate | 241 | 60.60% | 0.00% | 21.99% | 0.00% | AACACACAC: 14.11%; AACACAC: 3.32% |
| VI/Aromatic | 96 | 71.90% | 0.00% | 18.75% | 0.00% | AACACACAC: 8.33%; AACAC: 1.04% |
| Intermediate | 90 | 73.30% | 0.00% | 23.33% | 0.00% | AACACAC: 2.22%; AACACACAC: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318608236 | AACACACACAC -> AACAC | LOC_Os03g32540.1 | upstream_gene_variant ; 2952.0bp to feature; MODIFIER | silent_mutation | Average:20.789; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg0318608236 | AACACACACAC -> AACAC | LOC_Os03g32526.1 | intron_variant ; MODIFIER | silent_mutation | Average:20.789; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg0318608236 | AACACACACAC -> AACACACAC | LOC_Os03g32540.1 | upstream_gene_variant ; 2948.0bp to feature; MODIFIER | silent_mutation | Average:20.789; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg0318608236 | AACACACACAC -> AACACACAC | LOC_Os03g32526.1 | intron_variant ; MODIFIER | silent_mutation | Average:20.789; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg0318608236 | AACACACACAC -> DEL | N | N | silent_mutation | Average:20.789; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg0318608236 | AACACACACAC -> AAC | LOC_Os03g32540.1 | upstream_gene_variant ; 2954.0bp to feature; MODIFIER | silent_mutation | Average:20.789; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg0318608236 | AACACACACAC -> AAC | LOC_Os03g32526.1 | intron_variant ; MODIFIER | silent_mutation | Average:20.789; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg0318608236 | AACACACACAC -> A | LOC_Os03g32540.1 | upstream_gene_variant ; 2956.0bp to feature; MODIFIER | silent_mutation | Average:20.789; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg0318608236 | AACACACACAC -> A | LOC_Os03g32526.1 | intron_variant ; MODIFIER | silent_mutation | Average:20.789; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg0318608236 | AACACACACAC -> AACACAC | LOC_Os03g32540.1 | upstream_gene_variant ; 2950.0bp to feature; MODIFIER | silent_mutation | Average:20.789; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg0318608236 | AACACACACAC -> AACACAC | LOC_Os03g32526.1 | intron_variant ; MODIFIER | silent_mutation | Average:20.789; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |