| Variant ID: vg0111800114 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 11800114 |
| Reference Allele: G | Alternative Allele: A,GA |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTCGAGGGAGGTAATTTGTCCGGTTCGCATAGTTGGGGGTGAAGAATATCTGATATTGTGGTTTAGGGGGTAATTCGGACGACCGCGAGAGTTGGGGGGC[G/A,GA]
GGGGGTAATTCGTACTTTTTCATAAATAAAATACGTTTTCATAAATAAAATACGTGGGACTTGAGAGAGTTTCAGGTGAAGAACACTATTGGATATTAGA
TCTAATATCCAATAGTGTTCTTCACCTGAAACTCTCTCAAGTCCCACGTATTTTATTTATGAAAACGTATTTTATTTATGAAAAAGTACGAATTACCCCC[C/T,TC]
GCCCCCCAACTCTCGCGGTCGTCCGAATTACCCCCTAAACCACAATATCAGATATTCTTCACCCCCAACTATGCGAACCGGACAAATTACCTCCCTCGAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 55.00% | 4.30% | 16.59% | 24.12% | GA: 0.02% |
| All Indica | 2759 | 39.30% | 1.00% | 23.20% | 36.53% | NA |
| All Japonica | 1512 | 86.60% | 10.20% | 1.85% | 1.39% | NA |
| Aus | 269 | 40.90% | 7.10% | 28.62% | 23.42% | NA |
| Indica I | 595 | 27.40% | 0.20% | 36.47% | 35.97% | NA |
| Indica II | 465 | 21.90% | 0.20% | 22.37% | 55.48% | NA |
| Indica III | 913 | 51.90% | 1.40% | 16.76% | 29.90% | NA |
| Indica Intermediate | 786 | 43.90% | 1.50% | 21.12% | 33.46% | NA |
| Temperate Japonica | 767 | 77.40% | 19.60% | 1.96% | 1.04% | NA |
| Tropical Japonica | 504 | 96.20% | 0.00% | 1.79% | 1.98% | NA |
| Japonica Intermediate | 241 | 95.40% | 1.70% | 1.66% | 1.24% | NA |
| VI/Aromatic | 96 | 52.10% | 0.00% | 19.79% | 28.12% | NA |
| Intermediate | 90 | 50.00% | 3.30% | 22.22% | 23.33% | GA: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0111800114 | G -> A | LOC_Os01g21135.1 | upstream_gene_variant ; 4752.0bp to feature; MODIFIER | silent_mutation | Average:74.009; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |
| vg0111800114 | G -> A | LOC_Os01g21144.1 | downstream_gene_variant ; 125.0bp to feature; MODIFIER | silent_mutation | Average:74.009; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |
| vg0111800114 | G -> A | LOC_Os01g21160.1 | downstream_gene_variant ; 3997.0bp to feature; MODIFIER | silent_mutation | Average:74.009; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |
| vg0111800114 | G -> A | LOC_Os01g21160.2 | downstream_gene_variant ; 3997.0bp to feature; MODIFIER | silent_mutation | Average:74.009; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |
| vg0111800114 | G -> A | LOC_Os01g21160.4 | downstream_gene_variant ; 3997.0bp to feature; MODIFIER | silent_mutation | Average:74.009; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |
| vg0111800114 | G -> A | LOC_Os01g21135-LOC_Os01g21144 | intergenic_region ; MODIFIER | silent_mutation | Average:74.009; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |
| vg0111800114 | G -> DEL | N | N | silent_mutation | Average:74.009; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |
| vg0111800114 | G -> GA | LOC_Os01g21135.1 | upstream_gene_variant ; 4753.0bp to feature; MODIFIER | silent_mutation | Average:74.009; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |
| vg0111800114 | G -> GA | LOC_Os01g21144.1 | downstream_gene_variant ; 124.0bp to feature; MODIFIER | silent_mutation | Average:74.009; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |
| vg0111800114 | G -> GA | LOC_Os01g21160.1 | downstream_gene_variant ; 3996.0bp to feature; MODIFIER | silent_mutation | Average:74.009; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |
| vg0111800114 | G -> GA | LOC_Os01g21160.2 | downstream_gene_variant ; 3996.0bp to feature; MODIFIER | silent_mutation | Average:74.009; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |
| vg0111800114 | G -> GA | LOC_Os01g21160.4 | downstream_gene_variant ; 3996.0bp to feature; MODIFIER | silent_mutation | Average:74.009; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |
| vg0111800114 | G -> GA | LOC_Os01g21135-LOC_Os01g21144 | intergenic_region ; MODIFIER | silent_mutation | Average:74.009; most accessible tissue: Minghui63 young leaf, score: 85.028 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0111800114 | 5.03E-06 | 5.03E-06 | mr1373 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0111800114 | NA | 2.40E-07 | mr1648 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0111800114 | 7.57E-07 | 7.57E-07 | mr1172_2 | Jap_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0111800114 | NA | 8.09E-06 | mr1631_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |