| Variant ID: vg0623041409 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 23041409 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 73. )
AGCCTATGTCTTCGCCCCAAAGCCTTCGCACGTACCGCTTTCGCCCGGGTGCCCATCCGACGAGGTCTCTTCCAGCCCATACGGTTCTCTCTTCGACCTT[C/T]
GCCGCTTGCCTCCGGTCTGAGCTTGTTGCCTAAGCTTTTTGGTTTCGGTAGGTCCGGCCGAAGGCCCTTCGTGGTGTACCTCCAACACGTATAGAGCGTC
GACGCTCTATACGTGTTGGAGGTACACCACGAAGGGCCTTCGGCCGGACCTACCGAAACCAAAAAGCTTAGGCAACAAGCTCAGACCGGAGGCAAGCGGC[G/A]
AAGGTCGAAGAGAGAACCGTATGGGCTGGAAGAGACCTCGTCGGATGGGCACCCGGGCGAAAGCGGTACGTGCGAAGGCTTTGGGGCGAAGACATAGGCT
| 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 | 76.80% | 4.00% | 4.66% | 14.58% | NA |
| All Indica | 2759 | 71.50% | 6.70% | 7.39% | 14.32% | NA |
| All Japonica | 1512 | 89.90% | 0.00% | 0.20% | 9.92% | NA |
| Aus | 269 | 47.20% | 0.00% | 2.97% | 49.81% | NA |
| Indica I | 595 | 50.80% | 24.70% | 23.36% | 1.18% | NA |
| Indica II | 465 | 89.20% | 0.20% | 0.86% | 9.68% | NA |
| Indica III | 913 | 72.40% | 0.10% | 2.08% | 25.41% | NA |
| Indica Intermediate | 786 | 75.80% | 4.70% | 5.34% | 14.12% | NA |
| Temperate Japonica | 767 | 85.70% | 0.00% | 0.26% | 14.08% | NA |
| Tropical Japonica | 504 | 94.80% | 0.00% | 0.00% | 5.16% | NA |
| Japonica Intermediate | 241 | 92.90% | 0.00% | 0.41% | 6.64% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 1.04% | 6.25% | NA |
| Intermediate | 90 | 88.90% | 2.20% | 4.44% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0623041409 | C -> T | LOC_Os06g38810.1 | missense_variant ; p.Glu53Lys; MODERATE | nonsynonymous_codon ; E53K | Average:57.431; most accessible tissue: Minghui63 flag leaf, score: 72.028 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0623041409 | C -> DEL | LOC_Os06g38810.1 | N | frameshift_variant | Average:57.431; most accessible tissue: Minghui63 flag leaf, score: 72.028 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0623041409 | NA | 9.03E-06 | mr1201 | 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 |
| vg0623041409 | 9.88E-07 | NA | mr1234 | 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 |
| vg0623041409 | 4.77E-06 | 1.69E-08 | mr1234 | 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 |
| vg0623041409 | 5.04E-06 | NA | mr1237 | 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 |
| vg0623041409 | NA | 5.95E-07 | mr1274 | 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 |