| Variant ID: vg0200790320 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 790320 |
| Reference Allele: G | Alternative Allele: GT,GTTT,GCTTTTTTTAAACT |
| Primary Allele: G | Secondary Allele: GT |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 345. )
ACCACCTGATCATAAATTTCTCAAAACAATCAGCATCATGTAGATGAAATGGAACAATTGAAAATGCTCAATTTTGTTATTCTGTGACAGCTTGAGCTTT[G/GT,GTTT,GCTTTTTTTAAACT]
TTTTTTTTAACTTAAAAGACGTTGTTTTGTCTGAATTTCAAGGTAAAGTTCAGCTACAAGTTAGAACTAGCTTGGTTTTGTATCATCCTGTTCATAGAGA
TCTCTATGAACAGGATGATACAAAACCAAGCTAGTTCTAACTTGTAGCTGAACTTTACCTTGAAATTCAGACAAAACAACGTCTTTTAAGTTAAAAAAAA[C/AC,AAAC,AGTTTAAAAAAAGC]
AAAGCTCAAGCTGTCACAGAATAACAAAATTGAGCATTTTCAATTGTTCCATTTCATCTACATGATGCTGATTGTTTTGAGAAATTTATGATCAGGTGGT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.00% | 36.70% | 8.82% | 14.41% | GTTT: 0.08%; GCTTTTTTTAAACT: 0.04% |
| All Indica | 2759 | 10.60% | 51.90% | 13.74% | 23.60% | GTTT: 0.14% |
| All Japonica | 1512 | 94.60% | 1.70% | 1.92% | 1.72% | NA |
| Aus | 269 | 10.00% | 89.60% | 0.37% | 0.00% | NA |
| Indica I | 595 | 1.80% | 65.70% | 13.28% | 19.16% | NA |
| Indica II | 465 | 24.50% | 43.00% | 10.32% | 22.15% | NA |
| Indica III | 913 | 10.00% | 39.90% | 16.76% | 33.30% | GTTT: 0.11% |
| Indica Intermediate | 786 | 9.80% | 60.70% | 12.60% | 16.54% | GTTT: 0.38% |
| Temperate Japonica | 767 | 99.30% | 0.40% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 90.30% | 3.00% | 2.58% | 4.17% | NA |
| Japonica Intermediate | 241 | 88.80% | 3.30% | 6.22% | 1.66% | NA |
| VI/Aromatic | 96 | 83.30% | 16.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 64.40% | 20.00% | 8.89% | 4.44% | GCTTTTTTTAAACT: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0200790320 | G -> GCTTTTTTTAAACT | LOC_Os02g02350.2 | upstream_gene_variant ; 4645.0bp to feature; MODIFIER | silent_mutation | Average:64.566; most accessible tissue: Callus, score: 84.374 | N | N | N | N |
| vg0200790320 | G -> GCTTTTTTTAAACT | LOC_Os02g02360.1 | downstream_gene_variant ; 1086.0bp to feature; MODIFIER | silent_mutation | Average:64.566; most accessible tissue: Callus, score: 84.374 | N | N | N | N |
| vg0200790320 | G -> GCTTTTTTTAAACT | LOC_Os02g02380.1 | downstream_gene_variant ; 4745.0bp to feature; MODIFIER | silent_mutation | Average:64.566; most accessible tissue: Callus, score: 84.374 | N | N | N | N |
| vg0200790320 | G -> GCTTTTTTTAAACT | LOC_Os02g02370.1 | intron_variant ; MODIFIER | silent_mutation | Average:64.566; most accessible tissue: Callus, score: 84.374 | N | N | N | N |
| vg0200790320 | G -> GT | LOC_Os02g02350.2 | upstream_gene_variant ; 4645.0bp to feature; MODIFIER | silent_mutation | Average:64.566; most accessible tissue: Callus, score: 84.374 | N | N | N | N |
| vg0200790320 | G -> GT | LOC_Os02g02360.1 | downstream_gene_variant ; 1086.0bp to feature; MODIFIER | silent_mutation | Average:64.566; most accessible tissue: Callus, score: 84.374 | N | N | N | N |
| vg0200790320 | G -> GT | LOC_Os02g02380.1 | downstream_gene_variant ; 4745.0bp to feature; MODIFIER | silent_mutation | Average:64.566; most accessible tissue: Callus, score: 84.374 | N | N | N | N |
| vg0200790320 | G -> GT | LOC_Os02g02370.1 | intron_variant ; MODIFIER | silent_mutation | Average:64.566; most accessible tissue: Callus, score: 84.374 | N | N | N | N |
| vg0200790320 | G -> GTTT | LOC_Os02g02350.2 | upstream_gene_variant ; 4645.0bp to feature; MODIFIER | silent_mutation | Average:64.566; most accessible tissue: Callus, score: 84.374 | N | N | N | N |
| vg0200790320 | G -> GTTT | LOC_Os02g02360.1 | downstream_gene_variant ; 1086.0bp to feature; MODIFIER | silent_mutation | Average:64.566; most accessible tissue: Callus, score: 84.374 | N | N | N | N |
| vg0200790320 | G -> GTTT | LOC_Os02g02380.1 | downstream_gene_variant ; 4745.0bp to feature; MODIFIER | silent_mutation | Average:64.566; most accessible tissue: Callus, score: 84.374 | N | N | N | N |
| vg0200790320 | G -> GTTT | LOC_Os02g02370.1 | intron_variant ; MODIFIER | silent_mutation | Average:64.566; most accessible tissue: Callus, score: 84.374 | N | N | N | N |
| vg0200790320 | G -> DEL | N | N | silent_mutation | Average:64.566; most accessible tissue: Callus, score: 84.374 | N | N | N | N |