| Variant ID: vg1106565379 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 6565379 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GCTGTGGTTGCTCTCTCACCAACAACCGAGGATTAATTAATTGACCCGGTGTCGATGATGGTGCAGCAGGTGCAGGGGCCGATACTGGTGCTACCGGTTG[A/G]
GCCGATGGTGCATTGGGAGGAATCGGCTGGACAGCTGACTGATTATTAGTAATTAAGGGCCGATAATTTGGGAAAACACCTCCTGGTAAATAAACCGGTC
GACCGGTTTATTTACCAGGAGGTGTTTTCCCAAATTATCGGCCCTTAATTACTAATAATCAGTCAGCTGTCCAGCCGATTCCTCCCAATGCACCATCGGC[T/C]
CAACCGGTAGCACCAGTATCGGCCCCTGCACCTGCTGCACCATCATCGACACCGGGTCAATTAATTAATCCTCGGTTGTTGGTGAGAGAGCAACCACAGC
| 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 | 85.60% | 0.00% | 5.63% | 8.72% | NA |
| All Indica | 2759 | 86.50% | 0.00% | 9.24% | 4.20% | NA |
| All Japonica | 1512 | 80.70% | 0.00% | 0.60% | 18.72% | NA |
| Aus | 269 | 98.90% | 0.00% | 0.74% | 0.37% | NA |
| Indica I | 595 | 78.70% | 0.00% | 15.46% | 5.88% | NA |
| Indica II | 465 | 93.30% | 0.00% | 4.09% | 2.58% | NA |
| Indica III | 913 | 89.40% | 0.10% | 8.00% | 2.52% | NA |
| Indica Intermediate | 786 | 85.10% | 0.00% | 9.03% | 5.85% | NA |
| Temperate Japonica | 767 | 79.10% | 0.00% | 0.52% | 20.34% | NA |
| Tropical Japonica | 504 | 83.70% | 0.00% | 0.40% | 15.87% | NA |
| Japonica Intermediate | 241 | 79.30% | 0.00% | 1.24% | 19.50% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 0.00% | 0.00% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1106565379 | A -> DEL | LOC_Os11g11820.1 | N | frameshift_variant | Average:24.16; most accessible tissue: Zhenshan97 young leaf, score: 32.633 | N | N | N | N |
| vg1106565379 | A -> G | LOC_Os11g11820.1 | synonymous_variant ; p.Ala164Ala; LOW | synonymous_codon | Average:24.16; most accessible tissue: Zhenshan97 young leaf, score: 32.633 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1106565379 | NA | 7.03E-06 | mr1021 | 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 |
| vg1106565379 | NA | 5.17E-06 | mr1193 | 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 |
| vg1106565379 | NA | 9.48E-09 | mr1458 | 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 |
| vg1106565379 | NA | 3.27E-06 | mr1765 | 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 |
| vg1106565379 | 2.25E-06 | 2.25E-06 | mr1966 | 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 |