| Variant ID: vg0712338155 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 12338155 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTTCAGGAGTTCTACCTCTTTATTCTCAGCCTTCTGCAAGTAAATCTAGCTCTACACAGATATTACCTCTCATGCATTCATTGTTGAATAATATAATAGC[T/A]
TGCTGAGTACGTTGTACTCACCCTTGCTTCAACCCCTCTTTTTCAGAGTTTAATTGGAGTTTTTGCCGAAGCTGGGAGTTCAATCACATAAGTTAGTTCC
GGAACTAACTTATGTGATTGAACTCCCAGCTTCGGCAAAAACTCCAATTAAACTCTGAAAAAGAGGGGTTGAAGCAAGGGTGAGTACAACGTACTCAGCA[A/T]
GCTATTATATTATTCAACAATGAATGCATGAGAGGTAATATCTGTGTAGAGCTAGATTTACTTGCAGAAGGCTGAGAATAAAGAGGTAGAACTCCTGAAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.80% | 7.90% | 1.44% | 5.84% | NA |
| All Indica | 2759 | 98.80% | 0.00% | 0.62% | 0.58% | NA |
| All Japonica | 1512 | 58.20% | 24.10% | 2.71% | 15.01% | NA |
| Aus | 269 | 99.30% | 0.00% | 0.37% | 0.37% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | 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 | 95.80% | 0.10% | 2.16% | 1.91% | NA |
| Temperate Japonica | 767 | 68.40% | 2.20% | 3.91% | 25.42% | NA |
| Tropical Japonica | 504 | 31.70% | 66.50% | 1.59% | 0.20% | NA |
| Japonica Intermediate | 241 | 80.90% | 5.00% | 1.24% | 12.86% | NA |
| VI/Aromatic | 96 | 58.30% | 0.00% | 8.33% | 33.33% | NA |
| Intermediate | 90 | 90.00% | 8.90% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0712338155 | T -> DEL | N | N | silent_mutation | Average:53.481; most accessible tissue: Minghui63 flag leaf, score: 75.341 | N | N | N | N |
| vg0712338155 | T -> A | LOC_Os07g22080.1 | upstream_gene_variant ; 4153.0bp to feature; MODIFIER | silent_mutation | Average:53.481; most accessible tissue: Minghui63 flag leaf, score: 75.341 | N | N | N | N |
| vg0712338155 | T -> A | LOC_Os07g22060.1 | downstream_gene_variant ; 3593.0bp to feature; MODIFIER | silent_mutation | Average:53.481; most accessible tissue: Minghui63 flag leaf, score: 75.341 | N | N | N | N |
| vg0712338155 | T -> A | LOC_Os07g22070.1 | intron_variant ; MODIFIER | silent_mutation | Average:53.481; most accessible tissue: Minghui63 flag leaf, score: 75.341 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0712338155 | NA | 2.03E-06 | mr1194_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 |
| vg0712338155 | NA | 3.13E-07 | mr1363_2 | 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 |
| vg0712338155 | NA | 8.85E-06 | mr1786_2 | 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 |
| vg0712338155 | 1.00E-07 | NA | mr1850_2 | 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 |