| Variant ID: vg0611333425 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 11333425 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CGGTATCTCTCGACCTTAGTTCCTTTGCTCGCCGACACCGTCCAAAGGAAGCATAGAAAAACCAACGTCATTTGTCTTTGCACGAACAACTCCCAGCACA[C/A]
ACACATTTGATCCAATGACACTCAGGCCCCAAATCCAGTGTTGCGCTCCAACCATCGCTATTACTAGCACCTCTCCAACGATCACTTCATATGCTCTTCA
TGAAGAGCATATGAAGTGATCGTTGGAGAGGTGCTAGTAATAGCGATGGTTGGAGCGCAACACTGGATTTGGGGCCTGAGTGTCATTGGATCAAATGTGT[G/T]
TGTGCTGGGAGTTGTTCGTGCAAAGACAAATGACGTTGGTTTTTCTATGCTTCCTTTGGACGGTGTCGGCGAGCAAAGGAACTAAGGTCGAGAGATACCG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.70% | 4.70% | 4.21% | 8.42% | NA |
| All Indica | 2759 | 87.10% | 0.10% | 0.62% | 12.21% | NA |
| All Japonica | 1512 | 71.30% | 14.40% | 10.78% | 3.57% | NA |
| Aus | 269 | 94.40% | 0.00% | 5.58% | 0.00% | NA |
| Indica I | 595 | 98.70% | 0.20% | 0.67% | 0.50% | NA |
| Indica II | 465 | 99.10% | 0.00% | 0.22% | 0.65% | NA |
| Indica III | 913 | 69.40% | 0.00% | 0.22% | 30.34% | NA |
| Indica Intermediate | 786 | 91.70% | 0.10% | 1.27% | 6.87% | NA |
| Temperate Japonica | 767 | 57.90% | 25.80% | 16.30% | 0.00% | NA |
| Tropical Japonica | 504 | 84.70% | 1.80% | 3.17% | 10.32% | NA |
| Japonica Intermediate | 241 | 85.90% | 4.10% | 9.13% | 0.83% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 1.04% | 4.17% | NA |
| Intermediate | 90 | 90.00% | 3.30% | 3.33% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0611333425 | C -> A | LOC_Os06g19840.1 | upstream_gene_variant ; 749.0bp to feature; MODIFIER | silent_mutation | Average:59.038; most accessible tissue: Zhenshan97 young leaf, score: 81.6 | N | N | N | N |
| vg0611333425 | C -> A | LOC_Os06g19854.1 | downstream_gene_variant ; 3417.0bp to feature; MODIFIER | silent_mutation | Average:59.038; most accessible tissue: Zhenshan97 young leaf, score: 81.6 | N | N | N | N |
| vg0611333425 | C -> A | LOC_Os06g19840-LOC_Os06g19854 | intergenic_region ; MODIFIER | silent_mutation | Average:59.038; most accessible tissue: Zhenshan97 young leaf, score: 81.6 | N | N | N | N |
| vg0611333425 | C -> DEL | N | N | silent_mutation | Average:59.038; most accessible tissue: Zhenshan97 young leaf, score: 81.6 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0611333425 | NA | 1.53E-06 | mr1441 | 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 |
| vg0611333425 | NA | 5.64E-06 | mr1555 | 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 |
| vg0611333425 | NA | 3.83E-06 | mr1707 | 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 |
| vg0611333425 | NA | 6.80E-08 | mr1712 | 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 |
| vg0611333425 | 2.79E-06 | 2.79E-06 | mr1910 | 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 |
| vg0611333425 | NA | 3.28E-06 | mr1627_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 |