| Variant ID: vg0302880418 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 2880418 |
| Reference Allele: CGAAGAAGAAGAAGAA | Alternative Allele: CGAA,CGAAGAAGAAGAAGAAGAA,CGAAGAAGAA,CGAAGAA,CGAAGAAGAAGAA,C |
| Primary Allele: CGAA | Secondary Allele: CGAAGAAGAAGAAGAA |
Inferred Ancestral Allele: Not determined.
TTCAGCATGGCCGGCGCCGGCGCCGGCGGCGAGCCGGCGAAGAAGTCGACGGCGATGAAGAGCCAATCCTTCAGCATGGCGGGCCAGCCGCAACAGTAGA[CGAAGAAGAAGAAGAA/CGAA,CGAAGAAGAAGAAGAAGAA,CGAAGAAGAA,CGAAGAA,CGAAGAAGAAGAA,C]
GAAGAAGAAGAAGAAGAAGATGCCGCGCTGCTAGCTGAGCCGTTCGCACGGCGGCCTGATCGAGCGCGCATTGCCATTTATCGTTTTTGATTTTCTCACT
AGTGAGAAAATCAAAAACGATAAATGGCAATGCGCGCTCGATCAGGCCGCCGTGCGAACGGCTCAGCTAGCAGCGCGGCATCTTCTTCTTCTTCTTCTTC[TTCTTCTTCTTCTTCG/TTCG,TTCTTCTTCTTCTTCTTCG,TTCTTCTTCG,TTCTTCG,TTCTTCTTCTTCG,G]
TCTACTGTTGCGGCTGGCCCGCCATGCTGAAGGATTGGCTCTTCATCGCCGTCGACTTCTTCGCCGGCTCGCCGCCGGCGCCGGCGCCGGCCATGCTGAA
| Populations | Population Size | Frequency of CGAA(primary allele) | Frequency of CGAAGAAGAAGAAGAA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.30% | 33.10% | 4.91% | 0.17% | CGAAGAA: 3.47%; CGAAGAAGAAGAAGAAGAA: 1.65%; CGAAGAAGAA: 0.23%; CGAAGAAGAAGAA: 0.11%; C: 0.02% |
| All Indica | 2759 | 84.30% | 6.20% | 3.55% | 0.00% | CGAAGAA: 5.87% |
| All Japonica | 1512 | 0.40% | 85.80% | 8.00% | 0.53% | CGAAGAAGAAGAAGAAGAA: 4.83%; CGAAGAAGAAGAA: 0.33%; C: 0.07% |
| Aus | 269 | 91.10% | 5.20% | 0.74% | 0.00% | CGAAGAAGAA: 2.97% |
| Indica I | 595 | 86.60% | 4.90% | 7.23% | 0.00% | CGAAGAA: 1.34% |
| Indica II | 465 | 84.30% | 10.80% | 2.58% | 0.00% | CGAAGAA: 2.37% |
| Indica III | 913 | 89.00% | 2.70% | 0.33% | 0.00% | CGAAGAA: 7.89% |
| Indica Intermediate | 786 | 77.20% | 8.70% | 5.09% | 0.00% | CGAAGAA: 9.03% |
| Temperate Japonica | 767 | 0.30% | 79.80% | 11.60% | 1.04% | CGAAGAAGAAGAAGAAGAA: 6.65%; CGAAGAAGAAGAA: 0.65% |
| Tropical Japonica | 504 | 0.20% | 92.50% | 3.77% | 0.00% | CGAAGAAGAAGAAGAAGAA: 3.57% |
| Japonica Intermediate | 241 | 1.20% | 91.30% | 5.39% | 0.00% | CGAAGAAGAAGAAGAAGAA: 1.66%; C: 0.41% |
| VI/Aromatic | 96 | 49.00% | 43.80% | 3.12% | 0.00% | CGAAGAAGAAGAAGAAGAA: 4.17% |
| Intermediate | 90 | 41.10% | 43.30% | 8.89% | 0.00% | CGAAGAAGAA: 3.33%; CGAAGAA: 2.22%; CGAAGAAGAAGAAGAAGAA: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0302880418 | CGAAGAAGAAGAAGAA -> C | LOC_Os03g05770.1 | 3_prime_UTR_variant ; 23.0bp to feature; MODIFIER | silent_mutation | Average:67.678; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg0302880418 | CGAAGAAGAAGAAGAA -> C | LOC_Os03g05760.1 | downstream_gene_variant ; 4989.0bp to feature; MODIFIER | silent_mutation | Average:67.678; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg0302880418 | CGAAGAAGAAGAAGAA -> C | LOC_Os03g05780.1 | downstream_gene_variant ; 2586.0bp to feature; MODIFIER | silent_mutation | Average:67.678; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg0302880418 | CGAAGAAGAAGAAGAA -> CGAAGAA | LOC_Os03g05770.1 | 3_prime_UTR_variant ; 29.0bp to feature; MODIFIER | silent_mutation | Average:67.678; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg0302880418 | CGAAGAAGAAGAAGAA -> CGAAGAA | LOC_Os03g05760.1 | downstream_gene_variant ; 4995.0bp to feature; MODIFIER | silent_mutation | Average:67.678; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg0302880418 | CGAAGAAGAAGAAGAA -> CGAAGAA | LOC_Os03g05780.1 | downstream_gene_variant ; 2580.0bp to feature; MODIFIER | silent_mutation | Average:67.678; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg0302880418 | CGAAGAAGAAGAAGAA -> CGAAGAAGAA | LOC_Os03g05770.1 | 3_prime_UTR_variant ; 32.0bp to feature; MODIFIER | silent_mutation | Average:67.678; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg0302880418 | CGAAGAAGAAGAAGAA -> CGAAGAAGAA | LOC_Os03g05760.1 | downstream_gene_variant ; 4998.0bp to feature; MODIFIER | silent_mutation | Average:67.678; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg0302880418 | CGAAGAAGAAGAAGAA -> CGAAGAAGAA | LOC_Os03g05780.1 | downstream_gene_variant ; 2577.0bp to feature; MODIFIER | silent_mutation | Average:67.678; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg0302880418 | CGAAGAAGAAGAAGAA -> CGAAGAAGAAGAA | LOC_Os03g05770.1 | 3_prime_UTR_variant ; 35.0bp to feature; MODIFIER | silent_mutation | Average:67.678; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg0302880418 | CGAAGAAGAAGAAGAA -> CGAAGAAGAAGAA | LOC_Os03g05780.1 | downstream_gene_variant ; 2574.0bp to feature; MODIFIER | silent_mutation | Average:67.678; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg0302880418 | CGAAGAAGAAGAAGAA -> CGAAGAAGAAGAAGAAGAA | LOC_Os03g05770.1 | 3_prime_UTR_variant ; 38.0bp to feature; MODIFIER | silent_mutation | Average:67.678; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg0302880418 | CGAAGAAGAAGAAGAA -> CGAAGAAGAAGAAGAAGAA | LOC_Os03g05780.1 | downstream_gene_variant ; 2571.0bp to feature; MODIFIER | silent_mutation | Average:67.678; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg0302880418 | CGAAGAAGAAGAAGAA -> CGAA | LOC_Os03g05770.1 | 3_prime_UTR_variant ; 26.0bp to feature; MODIFIER | silent_mutation | Average:67.678; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg0302880418 | CGAAGAAGAAGAAGAA -> CGAA | LOC_Os03g05760.1 | downstream_gene_variant ; 4992.0bp to feature; MODIFIER | silent_mutation | Average:67.678; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg0302880418 | CGAAGAAGAAGAAGAA -> CGAA | LOC_Os03g05780.1 | downstream_gene_variant ; 2583.0bp to feature; MODIFIER | silent_mutation | Average:67.678; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg0302880418 | CGAAGAAGAAGAAGAA -> DEL | N | N | silent_mutation | Average:67.678; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |