| Variant ID: vg0622630104 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 22630104 |
| Reference Allele: A | Alternative Allele: G,T |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AAGGGATGAGGTTGCCATCTATCGAAAATTGTCCTGGATGTAGCGACGTCATTAAGAGCTTAAGCCGACCACATGATAGGGGTGATCGGCTGAGACAGAC[A/G,T]
AGACTCCCTGTTCATCAAAGATTGGGTCCAATGAGTCACGATCGTAATCAAGAGGACGAGTTGACCAGGAAGAATCAATGGTGTCCTTCTGGTATTTTTA
TAAAAATACCAGAAGGACACCATTGATTCTTCCTGGTCAACTCGTCCTCTTGATTACGATCGTGACTCATTGGACCCAATCTTTGATGAACAGGGAGTCT[T/C,A]
GTCTGTCTCAGCCGATCACCCCTATCATGTGGTCGGCTTAAGCTCTTAATGACGTCGCTACATCCAGGACAATTTTCGATAGATGGCAACCTCATCCCTT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 72.30% | 8.80% | 2.20% | 16.69% | T: 0.02% |
| All Indica | 2759 | 72.80% | 10.30% | 2.75% | 14.14% | NA |
| All Japonica | 1512 | 64.70% | 8.20% | 1.65% | 25.46% | NA |
| Aus | 269 | 98.50% | 0.40% | 0.74% | 0.00% | T: 0.37% |
| Indica I | 595 | 89.70% | 1.70% | 1.01% | 7.56% | NA |
| Indica II | 465 | 54.20% | 31.00% | 4.52% | 10.32% | NA |
| Indica III | 913 | 69.80% | 5.70% | 3.40% | 21.14% | NA |
| Indica Intermediate | 786 | 74.40% | 10.10% | 2.29% | 13.23% | NA |
| Temperate Japonica | 767 | 79.80% | 4.60% | 1.04% | 14.60% | NA |
| Tropical Japonica | 504 | 44.20% | 11.10% | 2.38% | 42.26% | NA |
| Japonica Intermediate | 241 | 59.30% | 13.70% | 2.07% | 24.90% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 75.60% | 7.80% | 1.11% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0622630104 | A -> G | LOC_Os06g38240.1 | synonymous_variant ; p.Thr769Thr; LOW | synonymous_codon | Average:28.144; most accessible tissue: Zhenshan97 flag leaf, score: 42.807 | N | N | N | N |
| vg0622630104 | A -> T | LOC_Os06g38240.1 | synonymous_variant ; p.Thr769Thr; LOW | synonymous_codon | Average:28.144; most accessible tissue: Zhenshan97 flag leaf, score: 42.807 | N | N | N | N |
| vg0622630104 | A -> DEL | LOC_Os06g38240.1 | N | frameshift_variant | Average:28.144; most accessible tissue: Zhenshan97 flag leaf, score: 42.807 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0622630104 | 8.17E-06 | 2.16E-07 | mr1123 | 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 |
| vg0622630104 | NA | 1.92E-06 | mr1240 | 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 |
| vg0622630104 | NA | 5.83E-06 | mr1496 | 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 |
| vg0622630104 | 2.19E-06 | 3.41E-08 | mr1936 | 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 |