| Variant ID: vg0324116659 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 24116659 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGGCCAACTCCAAATCATGGGTAGGGTAGTTGCCTTCATGGGGCCGTAGCTGGCGTGAGGCATAGGCTACCACATGACCTTCCTGCATTAATACGCACCC[C/T]
AATCCTTGGCGCGAAGCGTCACAGTACACCAGGTAGTCCTTGCGAGTATCCGGTAAGATCAACACTGGCGAGGAGACCAGCTTTTCATGAAGAGTTTGGA
TCCAAACTCTTCATGAAAAGCTGGTCTCCTCGCCAGTGTTGATCTTACCGGATACTCGCAAGGACTACCTGGTGTACTGTGACGCTTCGCGCCAAGGATT[G/A]
GGGTGCGTATTAATGCAGGAAGGTCATGTGGTAGCCTATGCCTCACGCCAGCTACGGCCCCATGAAGGCAACTACCCTACCCATGATTTGGAGTTGGCCG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.60% | 0.60% | 1.78% | 1.10% | NA |
| All Indica | 2759 | 96.00% | 0.00% | 2.46% | 1.56% | NA |
| All Japonica | 1512 | 97.90% | 1.70% | 0.26% | 0.07% | NA |
| Aus | 269 | 93.70% | 0.00% | 3.72% | 2.60% | NA |
| Indica I | 595 | 96.60% | 0.00% | 2.69% | 0.67% | NA |
| Indica II | 465 | 94.80% | 0.00% | 2.80% | 2.37% | NA |
| Indica III | 913 | 96.30% | 0.00% | 2.08% | 1.64% | NA |
| Indica Intermediate | 786 | 95.80% | 0.00% | 2.54% | 1.65% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 94.20% | 5.20% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 0.00% | 2.22% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0324116659 | C -> T | LOC_Os03g43250.1 | synonymous_variant ; p.Leu519Leu; LOW | synonymous_codon | Average:12.595; most accessible tissue: Minghui63 root, score: 17.665 | N | N | N | N |
| vg0324116659 | C -> DEL | LOC_Os03g43250.1 | N | frameshift_variant | Average:12.595; most accessible tissue: Minghui63 root, score: 17.665 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0324116659 | 1.76E-06 | 2.75E-06 | mr1018 | Ind_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 |
| vg0324116659 | 1.86E-06 | NA | mr1140 | Ind_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 |
| vg0324116659 | 1.62E-07 | 1.01E-06 | mr1395 | Ind_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 |
| vg0324116659 | 1.01E-06 | 4.71E-06 | mr1618 | Ind_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 |
| vg0324116659 | 3.10E-06 | 3.10E-06 | mr1778 | Ind_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 |