| Variant ID: vg0618738950 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 18738950 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCCCTAGCTTGAGTTTAATTATCTTCGATGTTTCAGAATTGATAATCAAATTAAACTCAAGATAGAATGGATGTCCAAAGGAAAAATTGTGCAAACCTGC[G/A]
CTCTGTATAAGATTATATAGAGGACGATTCATTGGTTCTGACTGTATCAATTTCCCTTGTGTGTTTCATCATGGCTCATCACTTCTGGGGTGATCTTGCT
AGCAAGATCACCCCAGAAGTGATGAGCCATGATGAAACACACAAGGGAAATTGATACAGTCAGAACCAATGAATCGTCCTCTATATAATCTTATACAGAG[C/T]
GCAGGTTTGCACAATTTTTCCTTTGGACATCCATTCTATCTTGAGTTTAATTTGATTATCAATTCTGAAACATCGAAGATAATTAAACTCAAGCTAGGGA
| 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 | 97.40% | 0.30% | 1.06% | 1.25% | NA |
| All Indica | 2759 | 99.70% | 0.00% | 0.11% | 0.18% | NA |
| All Japonica | 1512 | 92.80% | 1.10% | 2.98% | 3.17% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.00% | 0.00% | 0.34% | 0.67% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 91.30% | 1.00% | 3.39% | 4.30% | NA |
| Tropical Japonica | 504 | 97.40% | 0.60% | 1.39% | 0.60% | NA |
| Japonica Intermediate | 241 | 88.00% | 2.10% | 4.98% | 4.98% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 1.04% | 4.17% | NA |
| Intermediate | 90 | 96.70% | 0.00% | 1.11% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0618738950 | G -> A | LOC_Os06g32170.1 | upstream_gene_variant ; 4382.0bp to feature; MODIFIER | silent_mutation | Average:24.263; most accessible tissue: Minghui63 flag leaf, score: 39.69 | N | N | N | N |
| vg0618738950 | G -> A | LOC_Os06g32180.1 | downstream_gene_variant ; 47.0bp to feature; MODIFIER | silent_mutation | Average:24.263; most accessible tissue: Minghui63 flag leaf, score: 39.69 | N | N | N | N |
| vg0618738950 | G -> A | LOC_Os06g32170-LOC_Os06g32180 | intergenic_region ; MODIFIER | silent_mutation | Average:24.263; most accessible tissue: Minghui63 flag leaf, score: 39.69 | N | N | N | N |
| vg0618738950 | G -> DEL | N | N | silent_mutation | Average:24.263; most accessible tissue: Minghui63 flag leaf, score: 39.69 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0618738950 | 5.07E-06 | 5.07E-06 | mr1281_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 |
| vg0618738950 | NA | 4.98E-06 | mr1829_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 |
| vg0618738950 | 3.85E-09 | 5.74E-10 | mr1842_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 |