| Variant ID: vg0623034324 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 23034324 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TAAACATGAAATCAACAAAAGAAGTAAAAATATATATATATACGGACGCTCATGTGGGATATCATATTAGAGCTCCAAAGGGGACATATAAGTATTTGTC[G/A]
CTTTTTAAGATGCGATAATTAAGGATTTGTCACTCACTGTCCATAGCATGTGGGTCCAGTGGTAAATCCTTTTTCACCACTTGTAAGGGTTGTCAGTATC
GATACTGACAACCCTTACAAGTGGTGAAAAAGGATTTACCACTGGACCCACATGCTATGGACAGTGAGTGACAAATCCTTAATTATCGCATCTTAAAAAG[C/T]
GACAAATACTTATATGTCCCCTTTGGAGCTCTAATATGATATCCCACATGAGCGTCCGTATATATATATATTTTTACTTCTTTTGTTGATTTCATGTTTA
| 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 | 88.30% | 7.30% | 1.06% | 3.34% | NA |
| All Indica | 2759 | 93.80% | 0.60% | 0.04% | 5.58% | NA |
| All Japonica | 1512 | 76.30% | 21.20% | 2.31% | 0.20% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.20% | 0.17% | 0.00% | NA |
| Indica II | 465 | 91.40% | 1.30% | 0.00% | 7.31% | NA |
| Indica III | 913 | 89.80% | 0.50% | 0.00% | 9.64% | NA |
| Indica Intermediate | 786 | 95.30% | 0.60% | 0.00% | 4.07% | NA |
| Temperate Japonica | 767 | 62.30% | 34.80% | 2.48% | 0.39% | NA |
| Tropical Japonica | 504 | 92.70% | 4.80% | 2.58% | 0.00% | NA |
| Japonica Intermediate | 241 | 86.70% | 12.00% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 85.40% | 0.00% | 14.58% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 10.00% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0623034324 | G -> A | LOC_Os06g38800.1 | upstream_gene_variant ; 125.0bp to feature; MODIFIER | silent_mutation | Average:55.386; most accessible tissue: Callus, score: 74.961 | N | N | N | N |
| vg0623034324 | G -> A | LOC_Os06g38810.1 | downstream_gene_variant ; 4883.0bp to feature; MODIFIER | silent_mutation | Average:55.386; most accessible tissue: Callus, score: 74.961 | N | N | N | N |
| vg0623034324 | G -> A | LOC_Os06g38800-LOC_Os06g38810 | intergenic_region ; MODIFIER | silent_mutation | Average:55.386; most accessible tissue: Callus, score: 74.961 | N | N | N | N |
| vg0623034324 | G -> DEL | N | N | silent_mutation | Average:55.386; most accessible tissue: Callus, score: 74.961 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0623034324 | 2.06E-06 | NA | mr1305 | 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 |
| vg0623034324 | 7.12E-06 | 7.12E-06 | mr1610 | 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 |
| vg0623034324 | 6.57E-07 | 6.57E-07 | mr1649 | 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 |
| vg0623034324 | NA | 1.32E-06 | mr1977_2 | 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 |