| Variant ID: vg0141570346 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 41570346 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CAATGCGTGATGTTCTCGCTAGTTTTCCTAACTATCAATACCACATCTATAAAAGATGACAATCGATGACACAGTAAGCTACTCTTCTCAAAAACCATAT[C/A]
TGCTATCCTGCCTACTATTGGTAGAGACCCAATTTGGTGATGGGCCAAATAGACGGCCAACTTTTTTTGGTGGAGCAATTTTACAGTATTTGACTAGGTA
TACCTAGTCAAATACTGTAAAATTGCTCCACCAAAAAAAGTTGGCCGTCTATTTGGCCCATCACCAAATTGGGTCTCTACCAATAGTAGGCAGGATAGCA[G/T]
ATATGGTTTTTGAGAAGAGTAGCTTACTGTGTCATCGATTGTCATCTTTTATAGATGTGGTATTGATAGTTAGGAAAACTAGCGAGAACATCACGCATTG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 61.90% | 2.00% | 0.49% | 35.61% | NA |
| All Indica | 2759 | 39.70% | 0.10% | 0.76% | 59.41% | NA |
| All Japonica | 1512 | 92.70% | 5.90% | 0.07% | 1.32% | NA |
| Aus | 269 | 98.90% | 0.00% | 0.00% | 1.12% | NA |
| Indica I | 595 | 68.10% | 0.20% | 0.34% | 31.43% | NA |
| Indica II | 465 | 16.80% | 0.20% | 0.43% | 82.58% | NA |
| Indica III | 913 | 27.10% | 0.00% | 1.10% | 71.85% | NA |
| Indica Intermediate | 786 | 46.60% | 0.10% | 0.89% | 52.42% | NA |
| Temperate Japonica | 767 | 88.70% | 10.80% | 0.13% | 0.39% | NA |
| Tropical Japonica | 504 | 97.20% | 0.00% | 0.00% | 2.78% | NA |
| Japonica Intermediate | 241 | 96.30% | 2.50% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 73.30% | 4.40% | 1.11% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0141570346 | C -> A | LOC_Os01g71740.1 | upstream_gene_variant ; 3717.0bp to feature; MODIFIER | silent_mutation | Average:14.273; most accessible tissue: Callus, score: 72.802 | N | N | N | N |
| vg0141570346 | C -> A | LOC_Os01g71750.1 | upstream_gene_variant ; 2769.0bp to feature; MODIFIER | silent_mutation | Average:14.273; most accessible tissue: Callus, score: 72.802 | N | N | N | N |
| vg0141570346 | C -> A | LOC_Os01g71760.1 | downstream_gene_variant ; 404.0bp to feature; MODIFIER | silent_mutation | Average:14.273; most accessible tissue: Callus, score: 72.802 | N | N | N | N |
| vg0141570346 | C -> A | LOC_Os01g71770.1 | downstream_gene_variant ; 3561.0bp to feature; MODIFIER | silent_mutation | Average:14.273; most accessible tissue: Callus, score: 72.802 | N | N | N | N |
| vg0141570346 | C -> A | LOC_Os01g71750-LOC_Os01g71760 | intergenic_region ; MODIFIER | silent_mutation | Average:14.273; most accessible tissue: Callus, score: 72.802 | N | N | N | N |
| vg0141570346 | C -> DEL | N | N | silent_mutation | Average:14.273; most accessible tissue: Callus, score: 72.802 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0141570346 | 4.32E-06 | 5.00E-10 | mr1712 | 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 |
| vg0141570346 | 5.75E-07 | 5.75E-07 | mr1770 | 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 |
| vg0141570346 | NA | 6.28E-07 | mr1977 | 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 |