| Variant ID: vg1121000159 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 21000159 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 245. )
ACTAGCAAACTCTCAGCCTGAGAAGCCTCCGTTGCCTCATTTTTCTTTGATCTTCTCAAGTCTCGTGCAAGCAACGACGAAATTATCTCCTCAGTTTTGA[C/T]
AGTACCCTTGCCGTGTGTCAGGGTAGTCACCACATGTTCATAAGACGGTGGAAGCGAGCACAGAAGAATTATGGCCTTGTCTTTATCATCCAGTTTCACA
TGTGAAACTGGATGATAAAGACAAGGCCATAATTCTTCTGTGCTCGCTTCCACCGTCTTATGAACATGTGGTGACTACCCTGACACACGGCAAGGGTACT[G/A]
TCAAAACTGAGGAGATAATTTCGTCGTTGCTTGCACGAGACTTGAGAAGATCAAAGAAAAATGAGGCAACGGAGGCTTCTCAGGCTGAGAGTTTGCTAGT
| 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 | 92.80% | 0.50% | 1.23% | 5.48% | NA |
| All Indica | 2759 | 91.30% | 0.10% | 1.49% | 7.14% | NA |
| All Japonica | 1512 | 94.60% | 1.10% | 0.73% | 3.64% | NA |
| Aus | 269 | 97.80% | 0.70% | 1.12% | 0.37% | NA |
| Indica I | 595 | 92.60% | 0.50% | 0.84% | 6.05% | NA |
| Indica II | 465 | 89.00% | 0.00% | 1.29% | 9.68% | NA |
| Indica III | 913 | 93.30% | 0.00% | 1.53% | 5.15% | NA |
| Indica Intermediate | 786 | 89.20% | 0.00% | 2.04% | 8.78% | NA |
| Temperate Japonica | 767 | 96.00% | 2.10% | 0.39% | 1.56% | NA |
| Tropical Japonica | 504 | 90.90% | 0.00% | 1.39% | 7.74% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.41% | 1.66% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 0.00% | 3.12% | NA |
| Intermediate | 90 | 92.20% | 1.10% | 3.33% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1121000159 | C -> T | LOC_Os11g35770.1 | missense_variant ; p.Val156Ile; MODERATE | nonsynonymous_codon ; V156I | Average:33.448; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 | unknown | unknown | TOLERATED | 1.00 |
| vg1121000159 | C -> DEL | LOC_Os11g35770.1 | N | frameshift_variant | Average:33.448; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1121000159 | NA | 5.47E-06 | mr1574_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 |
| vg1121000159 | NA | 3.00E-07 | mr1662_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 |
| vg1121000159 | NA | 5.25E-07 | mr1742_2 | Ind_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 |
| vg1121000159 | NA | 8.75E-06 | mr1745_2 | Ind_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 |