| Variant ID: vg0600949542 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 949542 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATAGAGAGTGAAGAGGACAGAATTACCTGGAAGCTTACAAACCACAGTGAGTACAAGACGACGTCGATCTACAATGCACAATTCTTGCCTCAACAAAATC[G/A]
GACTTTGACGTACTCATCTGGAAACCCTGAGCGCCATGAAAGTGCAAGATCTTTACTTGGCTAGTGATCGAAAACAGGGTCTGGACATCCGACAGACTCG
CGAGTCTGTCGGATGTCCAGACCCTGTTTTCGATCACTAGCCAAGTAAAGATCTTGCACTTTCATGGCGCTCAGGGTTTCCAGATGAGTACGTCAAAGTC[C/T]
GATTTTGTTGAGGCAAGAATTGTGCATTGTAGATCGACGTCGTCTTGTACTCACTGTGGTTTGTAAGCTTCCAGGTAATTCTGTCCTCTTCACTCTCTAT
| 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 | 76.40% | 3.70% | 1.38% | 18.49% | NA |
| All Indica | 2759 | 75.50% | 1.30% | 1.16% | 21.96% | NA |
| All Japonica | 1512 | 85.60% | 8.70% | 1.85% | 3.77% | NA |
| Aus | 269 | 57.60% | 0.00% | 0.74% | 41.64% | NA |
| Indica I | 595 | 92.60% | 0.00% | 0.17% | 7.23% | NA |
| Indica II | 465 | 73.80% | 4.90% | 2.37% | 18.92% | NA |
| Indica III | 913 | 67.90% | 0.10% | 0.55% | 31.43% | NA |
| Indica Intermediate | 786 | 72.50% | 1.70% | 1.91% | 23.92% | NA |
| Temperate Japonica | 767 | 91.40% | 0.00% | 2.35% | 6.26% | NA |
| Tropical Japonica | 504 | 72.60% | 25.40% | 1.19% | 0.79% | NA |
| Japonica Intermediate | 241 | 94.60% | 1.70% | 1.66% | 2.07% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 1.04% | 89.58% | NA |
| Intermediate | 90 | 74.40% | 8.90% | 2.22% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0600949542 | G -> A | LOC_Os06g02660.1 | missense_variant ; p.Arg139Gln; MODERATE | nonsynonymous_codon ; R139Q | Average:60.648; most accessible tissue: Zhenshan97 young leaf, score: 83.199 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0600949542 | G -> DEL | LOC_Os06g02660.1 | N | frameshift_variant | Average:60.648; most accessible tissue: Zhenshan97 young leaf, score: 83.199 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0600949542 | NA | 4.78E-06 | mr1662 | 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 |
| vg0600949542 | 4.03E-06 | 5.89E-07 | mr1662_2 | 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 |