| Variant ID: vg0605309501 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 5309501 |
| Reference Allele: AGGG | Alternative Allele: GGGG,AG,A |
| Primary Allele: AGGG | Secondary Allele: GGGG |
Inferred Ancestral Allele: Not determined.
GGGGGACTATGTTGTAATACCCTAGAAAAATGTTGTTAGGTGAGGCATCCTGCAGCAACGTGGCCTTCATTGTATCCATCAGGAGACAGGATTTTGAAAA[AGGG/GGGG,AG,A]
GGGGGGGGGGAAGGTGATTGATTGGCTCGTTGAATTTTTGATGATTTTTATAATGTCTATTTCATAGTATTAATAGTAGTATGCACAAGAAATAAACGTG
CACGTTTATTTCTTGTGCATACTACTATTAATACTATGAAATAGACATTATAAAAATCATCAAAAATTCAACGAGCCAATCAATCACCTTCCCCCCCCCC[CCCT/CCCC,CT,T]
TTTTCAAAATCCTGTCTCCTGATGGATACAATGAAGGCCACGTTGCTGCAGGATGCCTCACCTAACAACATTTTTCTAGGGTATTACAACATAGTCCCCC
| Populations | Population Size | Frequency of AGGG(primary allele) | Frequency of GGGG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.90% | 10.60% | 17.20% | 11.89% | A: 1.76%; AG: 1.65% |
| All Indica | 2759 | 51.20% | 17.80% | 13.01% | 17.22% | A: 0.54%; AG: 0.25% |
| All Japonica | 1512 | 75.50% | 0.30% | 18.12% | 3.17% | AG: 2.78%; A: 0.13% |
| Aus | 269 | 24.20% | 0.40% | 36.43% | 7.06% | A: 24.16%; AG: 7.81% |
| Indica I | 595 | 40.30% | 33.30% | 13.11% | 13.28% | NA |
| Indica II | 465 | 51.00% | 0.40% | 13.12% | 35.48% | NA |
| Indica III | 913 | 58.70% | 19.80% | 10.62% | 10.19% | A: 0.66% |
| Indica Intermediate | 786 | 50.90% | 13.90% | 15.65% | 17.56% | A: 1.15%; AG: 0.89% |
| Temperate Japonica | 767 | 70.90% | 0.00% | 23.99% | 4.43% | AG: 0.52%; A: 0.13% |
| Tropical Japonica | 504 | 81.50% | 0.80% | 9.52% | 1.39% | AG: 6.55%; A: 0.20% |
| Japonica Intermediate | 241 | 77.60% | 0.00% | 17.43% | 2.90% | AG: 2.07% |
| VI/Aromatic | 96 | 25.00% | 2.10% | 60.42% | 6.25% | AG: 5.21%; A: 1.04% |
| Intermediate | 90 | 50.00% | 4.40% | 26.67% | 15.56% | AG: 3.33% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0605309501 | AGGG -> AG | LOC_Os06g10320.1 | downstream_gene_variant ; 2772.0bp to feature; MODIFIER | silent_mutation | Average:74.907; most accessible tissue: Minghui63 young leaf, score: 84.814 | N | N | N | N |
| vg0605309501 | AGGG -> AG | LOC_Os06g10330.1 | downstream_gene_variant ; 1756.0bp to feature; MODIFIER | silent_mutation | Average:74.907; most accessible tissue: Minghui63 young leaf, score: 84.814 | N | N | N | N |
| vg0605309501 | AGGG -> AG | LOC_Os06g10340.1 | intron_variant ; MODIFIER | silent_mutation | Average:74.907; most accessible tissue: Minghui63 young leaf, score: 84.814 | N | N | N | N |
| vg0605309501 | AGGG -> A | LOC_Os06g10320.1 | downstream_gene_variant ; 2771.0bp to feature; MODIFIER | silent_mutation | Average:74.907; most accessible tissue: Minghui63 young leaf, score: 84.814 | N | N | N | N |
| vg0605309501 | AGGG -> A | LOC_Os06g10330.1 | downstream_gene_variant ; 1755.0bp to feature; MODIFIER | silent_mutation | Average:74.907; most accessible tissue: Minghui63 young leaf, score: 84.814 | N | N | N | N |
| vg0605309501 | AGGG -> A | LOC_Os06g10340.1 | intron_variant ; MODIFIER | silent_mutation | Average:74.907; most accessible tissue: Minghui63 young leaf, score: 84.814 | N | N | N | N |
| vg0605309501 | AGGG -> DEL | N | N | silent_mutation | Average:74.907; most accessible tissue: Minghui63 young leaf, score: 84.814 | N | N | N | N |
| vg0605309501 | AGGG -> GGGG | LOC_Os06g10320.1 | downstream_gene_variant ; 2770.0bp to feature; MODIFIER | silent_mutation | Average:74.907; most accessible tissue: Minghui63 young leaf, score: 84.814 | N | N | N | N |
| vg0605309501 | AGGG -> GGGG | LOC_Os06g10330.1 | downstream_gene_variant ; 1754.0bp to feature; MODIFIER | silent_mutation | Average:74.907; most accessible tissue: Minghui63 young leaf, score: 84.814 | N | N | N | N |
| vg0605309501 | AGGG -> GGGG | LOC_Os06g10340.1 | intron_variant ; MODIFIER | silent_mutation | Average:74.907; most accessible tissue: Minghui63 young leaf, score: 84.814 | N | N | N | N |