| Variant ID: vg1108497933 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 8497933 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCAATGGACAGGTGGAGCGAGCCAACGGCATGATACTTCAAGGGATTAAAGCGCGAGTTTTTGACCGGCTAAAACCCTATGCCGGCAAATGGGTGAAACA[G/A]
CTACCATCAGTGCTTTGGTCTTTGCGTACTACACCCAGTCGGGCCACAGGCCAGTCGCCTTTTTTCCTTGTCTATGGGGCAGAAGCAATGTTGCCGAGTG
CACTCGGCAACATTGCTTCTGCCCCATAGACAAGGAAAAAAGGCGACTGGCCTGTGGCCCGACTGGGTGTAGTACGCAAAGACCAAAGCACTGATGGTAG[C/T]
TGTTTCACCCATTTGCCGGCATAGGGTTTTAGCCGGTCAAAAACTCGCGCTTTAATCCCTTGAAGTATCATGCCGTTGGCTCGCTCCACCTGTCCATTGC
| 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 | 88.60% | 4.10% | 6.14% | 1.10% | NA |
| All Indica | 2759 | 81.60% | 7.10% | 9.64% | 1.74% | NA |
| All Japonica | 1512 | 99.10% | 0.00% | 0.66% | 0.26% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 85.00% | 3.00% | 11.60% | 0.34% | NA |
| Indica II | 465 | 83.40% | 6.50% | 7.53% | 2.58% | NA |
| Indica III | 913 | 78.10% | 10.70% | 9.42% | 1.75% | NA |
| Indica Intermediate | 786 | 81.80% | 6.20% | 9.67% | 2.29% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.52% | 0.13% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.99% | 0.20% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.41% | 0.83% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 0.00% | 14.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1108497933 | G -> A | LOC_Os11g15090.1 | synonymous_variant ; p.Gln1791Gln; LOW | synonymous_codon | Average:13.586; most accessible tissue: Minghui63 root, score: 27.443 | N | N | N | N |
| vg1108497933 | G -> DEL | LOC_Os11g15090.1 | N | frameshift_variant | Average:13.586; most accessible tissue: Minghui63 root, score: 27.443 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1108497933 | 4.95E-07 | NA | mr1489 | 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 |
| vg1108497933 | 4.48E-07 | 4.48E-07 | mr1778 | 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 |