| Variant ID: vg0402111447 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2111447 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GGTGCATCACGTCGATTGCGTGGCGGACGTCCAAGAATTCCCACTAGGGTAACTCCCAAAATATGGAGTTTTTTTTCCACATCGCCGCGTGACCATCTTC[A/G]
CTCTCTATAGGCTGGCTGCCAGGCTCCTTTCCAAACACTACTTTAAGATCTTTAACCATAGCAAACACTGTTTTCCCGCTGCGTACGGTGGTCCGCCGTA
TACGGCGGACCACCGTACGCAGCGGGAAAACAGTGTTTGCTATGGTTAAAGATCTTAAAGTAGTGTTTGGAAAGGAGCCTGGCAGCCAGCCTATAGAGAG[T/C]
GAAGATGGTCACGCGGCGATGTGGAAAAAAAACTCCATATTTTGGGAGTTACCCTAGTGGGAATTCTTGGACGTCCGCCACGCAATCGACGTGATGCACC
| 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 | 18.50% | 14.20% | 6.64% | 60.64% | NA |
| All Indica | 2759 | 9.50% | 12.30% | 8.55% | 69.66% | NA |
| All Japonica | 1512 | 34.00% | 20.30% | 0.73% | 44.97% | NA |
| Aus | 269 | 19.70% | 0.00% | 17.84% | 62.45% | NA |
| Indica I | 595 | 16.30% | 2.50% | 8.07% | 73.11% | NA |
| Indica II | 465 | 9.20% | 1.70% | 5.59% | 83.44% | NA |
| Indica III | 913 | 6.70% | 22.70% | 10.51% | 60.13% | NA |
| Indica Intermediate | 786 | 7.60% | 14.00% | 8.40% | 69.97% | NA |
| Temperate Japonica | 767 | 59.60% | 27.60% | 0.13% | 12.65% | NA |
| Tropical Japonica | 504 | 3.60% | 14.90% | 1.39% | 80.16% | NA |
| Japonica Intermediate | 241 | 16.20% | 8.30% | 1.24% | 74.27% | NA |
| VI/Aromatic | 96 | 30.20% | 10.40% | 13.54% | 45.83% | NA |
| Intermediate | 90 | 18.90% | 16.70% | 6.67% | 57.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402111447 | A -> DEL | N | N | silent_mutation | Average:7.519; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg0402111447 | A -> G | LOC_Os04g04420.1 | upstream_gene_variant ; 4985.0bp to feature; MODIFIER | silent_mutation | Average:7.519; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg0402111447 | A -> G | LOC_Os04g04440.1 | upstream_gene_variant ; 2993.0bp to feature; MODIFIER | silent_mutation | Average:7.519; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg0402111447 | A -> G | LOC_Os04g04430.1 | intron_variant ; MODIFIER | silent_mutation | Average:7.519; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402111447 | 3.82E-08 | NA | mr1115_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 |
| vg0402111447 | 6.62E-06 | NA | mr1566_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 |
| vg0402111447 | 3.56E-07 | NA | mr1611_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 |