| Variant ID: vg0213362443 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 13362443 |
| Reference Allele: G | Alternative Allele: GCCC,GCCCC,GC,GCC,GCCCCC,C |
| Primary Allele: G | Secondary Allele: GCC |
Inferred Ancestral Allele: Not determined.
GAGTGACAGCCAAAAGCAAGCTCAACATTGCAATGGGGAAATTGCGATTAGGGAAATCTTGCCCGTGATTGCAATTTCGGAACAAAATTTTCAAAATTTT[G/GCCC,GCCCC,GC,GCC,GCCCCC,C]
CCTCCCCCCCCACCGGCAAGCATATATCTCACCCGAAATTTCTCCTTTTTTCATGTTTTTGTGAATTTGGTCAAAGTTTATTCTAAATCATTCAAAATTC
GAATTTTGAATGATTTAGAATAAACTTTGACCAAATTCACAAAAACATGAAAAAAGGAGAAATTTCGGGTGAGATATATGCTTGCCGGTGGGGGGGGAGG[C/GGGC,GGGGC,GC,GGC,GGGGGC,G]
AAAATTTTGAAAATTTTGTTCCGAAATTGCAATCACGGGCAAGATTTCCCTAATCGCAATTTCCCCATTGCAATGTTGAGCTTGCTTTTGGCTGTCACTC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GCC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 39.50% | 2.80% | 50.23% | 3.34% | GC: 2.48%; GCCC: 1.14%; GCCCC: 0.40%; C: 0.04%; GCCCCC: 0.04% |
| All Indica | 2759 | 10.40% | 4.30% | 74.70% | 4.89% | GC: 3.15%; GCCC: 1.78%; GCCCC: 0.58%; C: 0.07%; GCCCCC: 0.07% |
| All Japonica | 1512 | 92.90% | 0.00% | 5.56% | 1.39% | GCCCC: 0.13% |
| Aus | 269 | 17.10% | 4.10% | 66.17% | 0.00% | GC: 10.41%; GCCC: 1.86%; GCCCC: 0.37% |
| Indica I | 595 | 5.70% | 3.50% | 83.03% | 4.03% | GC: 2.18%; GCCC: 1.18%; GCCCC: 0.34% |
| Indica II | 465 | 13.10% | 4.30% | 74.84% | 2.37% | GC: 2.58%; GCCC: 2.15%; GCCCC: 0.43%; C: 0.22% |
| Indica III | 913 | 11.90% | 5.80% | 67.91% | 7.01% | GC: 3.40%; GCCC: 2.63%; GCCCC: 0.99%; GCCCCC: 0.22%; C: 0.11% |
| Indica Intermediate | 786 | 10.60% | 3.30% | 76.21% | 4.58% | GC: 3.94%; GCCC: 1.02%; GCCCC: 0.38% |
| Temperate Japonica | 767 | 97.70% | 0.00% | 1.83% | 0.39% | GCCCC: 0.13% |
| Tropical Japonica | 504 | 87.10% | 0.00% | 9.72% | 2.98% | GCCCC: 0.20% |
| Japonica Intermediate | 241 | 90.00% | 0.00% | 8.71% | 1.24% | NA |
| VI/Aromatic | 96 | 80.20% | 1.00% | 18.75% | 0.00% | NA |
| Intermediate | 90 | 57.80% | 1.10% | 36.67% | 2.22% | GC: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0213362443 | G -> GCCCC | LOC_Os02g22374.4 | upstream_gene_variant ; 667.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCCCC | LOC_Os02g22370.1 | downstream_gene_variant ; 1792.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCCCC | LOC_Os02g22370.3 | downstream_gene_variant ; 4192.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCCCC | LOC_Os02g22370.2 | downstream_gene_variant ; 2638.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCCCC | LOC_Os02g22374.2 | downstream_gene_variant ; 543.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCCCC | LOC_Os02g22374.1 | intron_variant ; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCCCC | LOC_Os02g22374.3 | intron_variant ; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> DEL | N | N | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCCCCC | LOC_Os02g22374.4 | upstream_gene_variant ; 667.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCCCCC | LOC_Os02g22370.1 | downstream_gene_variant ; 1792.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCCCCC | LOC_Os02g22370.3 | downstream_gene_variant ; 4192.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCCCCC | LOC_Os02g22370.2 | downstream_gene_variant ; 2638.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCCCCC | LOC_Os02g22374.2 | downstream_gene_variant ; 543.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCCCCC | LOC_Os02g22374.1 | intron_variant ; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCCCCC | LOC_Os02g22374.3 | intron_variant ; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> C | LOC_Os02g22374.4 | upstream_gene_variant ; 666.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> C | LOC_Os02g22370.1 | downstream_gene_variant ; 1791.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> C | LOC_Os02g22370.3 | downstream_gene_variant ; 4191.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> C | LOC_Os02g22370.2 | downstream_gene_variant ; 2637.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> C | LOC_Os02g22374.2 | downstream_gene_variant ; 544.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> C | LOC_Os02g22374.1 | intron_variant ; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> C | LOC_Os02g22374.3 | intron_variant ; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GC | LOC_Os02g22374.4 | upstream_gene_variant ; 667.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GC | LOC_Os02g22370.1 | downstream_gene_variant ; 1792.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GC | LOC_Os02g22370.3 | downstream_gene_variant ; 4192.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GC | LOC_Os02g22370.2 | downstream_gene_variant ; 2638.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GC | LOC_Os02g22374.2 | downstream_gene_variant ; 543.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GC | LOC_Os02g22374.1 | intron_variant ; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GC | LOC_Os02g22374.3 | intron_variant ; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCC | LOC_Os02g22374.4 | upstream_gene_variant ; 667.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCC | LOC_Os02g22370.1 | downstream_gene_variant ; 1792.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCC | LOC_Os02g22370.3 | downstream_gene_variant ; 4192.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCC | LOC_Os02g22370.2 | downstream_gene_variant ; 2638.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCC | LOC_Os02g22374.2 | downstream_gene_variant ; 543.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCC | LOC_Os02g22374.1 | intron_variant ; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCC | LOC_Os02g22374.3 | intron_variant ; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCCC | LOC_Os02g22374.4 | upstream_gene_variant ; 667.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCCC | LOC_Os02g22370.1 | downstream_gene_variant ; 1792.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCCC | LOC_Os02g22370.3 | downstream_gene_variant ; 4192.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCCC | LOC_Os02g22370.2 | downstream_gene_variant ; 2638.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCCC | LOC_Os02g22374.2 | downstream_gene_variant ; 543.0bp to feature; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCCC | LOC_Os02g22374.1 | intron_variant ; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
| vg0213362443 | G -> GCCC | LOC_Os02g22374.3 | intron_variant ; MODIFIER | silent_mutation | Average:47.371; most accessible tissue: Zhenshan97 flower, score: 66.02 | N | N | N | N |
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