| Variant ID: vg0100792291 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 792291 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AAGTATTCACTGGGCAGAACTTATTGATTGGTACGGAAATGACACAGGATGAAAAATACAAAGTGAGGAAACTGGCAATTGTGGCACTATGGTGCATTCA[G/A]
TGGAACCCCAAAAACAGGCCATCAACGACCCAGGTGGTTAACATGCTAACAGGAAGGTTGCAGGATCTGCAGATGCCTCCTAAACCATTTGTCTCATCTG
CAGATGAGACAAATGGTTTAGGAGGCATCTGCAGATCCTGCAACCTTCCTGTTAGCATGTTAACCACCTGGGTCGTTGATGGCCTGTTTTTGGGGTTCCA[C/T]
TGAATGCACCATAGTGCCACAATTGCCAGTTTCCTCACTTTGTATTTTTCATCCTGTGTCATTTCCGTACCAATCAATAAGTTCTGCCCAGTGAATACTT
| 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 | 57.10% | 38.20% | 0.55% | 4.15% | NA |
| All Indica | 2759 | 68.00% | 30.80% | 0.18% | 1.01% | NA |
| All Japonica | 1512 | 44.20% | 53.30% | 1.12% | 1.39% | NA |
| Aus | 269 | 37.20% | 18.60% | 0.37% | 43.87% | NA |
| Indica I | 595 | 31.60% | 68.20% | 0.17% | 0.00% | NA |
| Indica II | 465 | 94.20% | 5.80% | 0.00% | 0.00% | NA |
| Indica III | 913 | 73.80% | 25.10% | 0.22% | 0.88% | NA |
| Indica Intermediate | 786 | 73.20% | 24.00% | 0.25% | 2.54% | NA |
| Temperate Japonica | 767 | 68.80% | 27.40% | 1.56% | 2.22% | NA |
| Tropical Japonica | 504 | 6.00% | 93.70% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 45.60% | 51.50% | 1.24% | 1.66% | NA |
| VI/Aromatic | 96 | 10.40% | 64.60% | 3.12% | 21.88% | NA |
| Intermediate | 90 | 50.00% | 41.10% | 0.00% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100792291 | G -> A | LOC_Os01g02440.1 | synonymous_variant ; p.Gln522Gln; LOW | synonymous_codon | Average:48.405; most accessible tissue: Minghui63 flag leaf, score: 60.569 | N | N | N | N |
| vg0100792291 | G -> DEL | LOC_Os01g02440.1 | N | frameshift_variant | Average:48.405; most accessible tissue: Minghui63 flag leaf, score: 60.569 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0100792291 | NA | 3.91E-08 | mr1310_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 |
| vg0100792291 | NA | 9.26E-07 | mr1389_2 | 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 |
| vg0100792291 | NA | 8.12E-06 | mr1398_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 |