| Variant ID: vg0402826180 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2826180 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AACAAAAACGGCTTATAAAAGCACGTAGGCTCTCTATATATAGCCGATCAGCTTCCAGCTCTTCATCCCAGCTTGCATCGTTACCAATTCCACCTTCACT[C/T]
GACCACTCCAACAAAACATGGACATCTCTCACCTCCTCCTACGCTTCTTCCTCCTCCTCCTCCTCCTCCTCCTCGCCTTCTCGCTCGACGATGCTCCCCA
TGGGGAGCATCGTCGAGCGAGAAGGCGAGGAGGAGGAGGAGGAGGAGGAGGAAGAAGCGTAGGAGGAGGTGAGAGATGTCCATGTTTTGTTGGAGTGGTC[G/A]
AGTGAAGGTGGAATTGGTAACGATGCAAGCTGGGATGAAGAGCTGGAAGCTGATCGGCTATATATAGAGAGCCTACGTGCTTTTATAAGCCGTTTTTGTT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.40% | 6.00% | 0.91% | 0.76% | NA |
| All Indica | 2759 | 95.00% | 4.70% | 0.11% | 0.22% | NA |
| All Japonica | 1512 | 97.60% | 0.30% | 1.98% | 0.13% | NA |
| Aus | 269 | 36.80% | 53.20% | 2.60% | 7.43% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.30% | 3.40% | 0.00% | 0.22% | NA |
| Indica III | 913 | 91.60% | 8.20% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 94.40% | 4.80% | 0.13% | 0.64% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.65% | 0.00% | NA |
| Tropical Japonica | 504 | 97.60% | 0.40% | 1.59% | 0.40% | NA |
| Japonica Intermediate | 241 | 92.10% | 0.80% | 7.05% | 0.00% | NA |
| VI/Aromatic | 96 | 88.50% | 2.10% | 2.08% | 7.29% | NA |
| Intermediate | 90 | 93.30% | 4.40% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402826180 | C -> DEL | N | N | silent_mutation | Average:51.032; most accessible tissue: Zhenshan97 young leaf, score: 59.612 | N | N | N | N |
| vg0402826180 | C -> T | LOC_Os04g05580.1 | 5_prime_UTR_premature_start_codon_gain_variant ; LOW | silent_mutation | Average:51.032; most accessible tissue: Zhenshan97 young leaf, score: 59.612 | N | N | N | N |
| vg0402826180 | C -> T | LOC_Os04g05580.1 | 5_prime_UTR_variant ; 18.0bp to feature; MODIFIER | silent_mutation | Average:51.032; most accessible tissue: Zhenshan97 young leaf, score: 59.612 | N | N | N | N |
| vg0402826180 | C -> T | LOC_Os04g05570.1 | upstream_gene_variant ; 4287.0bp to feature; MODIFIER | silent_mutation | Average:51.032; most accessible tissue: Zhenshan97 young leaf, score: 59.612 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402826180 | 1.57E-06 | NA | mr1111 | 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 |
| vg0402826180 | NA | 5.80E-08 | mr1126 | 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 |
| vg0402826180 | NA | 1.72E-06 | mr1382 | 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 |
| vg0402826180 | NA | 1.54E-06 | mr1523 | 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 |
| vg0402826180 | 9.07E-06 | NA | mr1144_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 |