| Variant ID: vg0408863993 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 8863993 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCTGAGCTTATGACTCGACCATCTGAAAAGGATAGATATGGATGCTGAGTTTCATACTGTTTGGCGTGCTATAGGTTGGGATAAATTTGCATGTGTAGAC[G/A]
AGCCGGGTTCCCGTTTGCTTACCATGCAATGTTTATGTGCCTTGCTAGAGGTAGGCGATGGTGTTACTTTCCGGTTATTCTGCAAGGAATATCACCTTCC
GGAAGGTGATATTCCTTGCAGAATAACCGGAAAGTAACACCATCGCCTACCTCTAGCAAGGCACATAAACATTGCATGGTAAGCAAACGGGAACCCGGCT[C/T]
GTCTACACATGCAAATTTATCCCAACCTATAGCACGCCAAACAGTATGAAACTCAGCATCCATATCTATCCTTTTCAGATGGTCGAGTCATAAGCTCAGG
| 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 | 35.50% | 2.10% | 3.28% | 59.14% | NA |
| All Indica | 2759 | 5.90% | 0.00% | 3.37% | 90.72% | NA |
| All Japonica | 1512 | 90.30% | 6.30% | 2.51% | 0.86% | NA |
| Aus | 269 | 6.30% | 0.00% | 6.69% | 86.99% | NA |
| Indica I | 595 | 3.20% | 0.00% | 4.71% | 92.10% | NA |
| Indica II | 465 | 8.80% | 0.00% | 4.73% | 86.45% | NA |
| Indica III | 913 | 4.80% | 0.00% | 1.53% | 93.65% | NA |
| Indica Intermediate | 786 | 7.40% | 0.10% | 3.69% | 88.80% | NA |
| Temperate Japonica | 767 | 84.70% | 11.00% | 4.04% | 0.26% | NA |
| Tropical Japonica | 504 | 97.20% | 1.60% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 93.80% | 1.20% | 2.90% | 2.07% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 1.04% | 11.46% | NA |
| Intermediate | 90 | 54.40% | 2.20% | 5.56% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0408863993 | G -> DEL | LOC_Os04g16314.1 | N | frameshift_variant | Average:7.928; most accessible tissue: Callus, score: 33.316 | N | N | N | N |
| vg0408863993 | G -> A | LOC_Os04g16314.1 | missense_variant ; p.Glu234Lys; MODERATE | nonsynonymous_codon ; E234K | Average:7.928; most accessible tissue: Callus, score: 33.316 | unknown | unknown | TOLERATED | 0.56 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0408863993 | 2.78E-07 | 7.24E-09 | mr1035 | 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 |
| vg0408863993 | 5.95E-06 | 1.93E-11 | mr1062 | 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 |
| vg0408863993 | 2.98E-07 | 2.98E-07 | mr1525 | 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 |
| vg0408863993 | 1.12E-06 | 8.28E-08 | mr1626 | 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 |
| vg0408863993 | NA | 2.37E-06 | mr1035_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 |
| vg0408863993 | 4.44E-07 | 1.00E-10 | mr1062_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 |
| vg0408863993 | 3.33E-06 | 1.81E-10 | mr1631_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 |