| Variant ID: vg1000973578 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 973578 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GAACGGGAAGAATCTGAGTTTATATCATCTTCCAGAGCATTGAAATCAGATTCAGTAATTTTGCTGCCAGGGATAAGGATTTTTTATATACCTGCCAACT[T/C]
CTTCAGCCTTTTAGCCGATTTTCCCCTTTGTTTGCCAATTCCCATTCGATGATCAAATTTGAGCTCTTGGTTGGCATTAAGAAGCCTAGAGCTCTACCTT
AAGGTAGAGCTCTAGGCTTCTTAATGCCAACCAAGAGCTCAAATTTGATCATCGAATGGGAATTGGCAAACAAAGGGGAAAATCGGCTAAAAGGCTGAAG[A/G]
AGTTGGCAGGTATATAAAAAATCCTTATCCCTGGCAGCAAAATTACTGAATCTGATTTCAATGCTCTGGAAGATGATATAAACTCAGATTCTTCCCGTTC
| 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 | 93.50% | 2.30% | 4.23% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.10% | 0.18% | 0.00% | NA |
| All Japonica | 1512 | 80.80% | 6.70% | 12.50% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.40% | 0.37% | 0.00% | NA |
| Indica I | 595 | 99.30% | 0.20% | 0.50% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.40% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 66.80% | 12.60% | 20.60% | 0.00% | NA |
| Tropical Japonica | 504 | 97.60% | 0.00% | 2.38% | 0.00% | NA |
| Japonica Intermediate | 241 | 90.50% | 1.70% | 7.88% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 3.30% | 5.56% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000973578 | T -> C | LOC_Os10g02560.1 | upstream_gene_variant ; 4480.0bp to feature; MODIFIER | silent_mutation | Average:74.249; most accessible tissue: Minghui63 young leaf, score: 85.236 | N | N | N | N |
| vg1000973578 | T -> C | LOC_Os10g02570.1 | upstream_gene_variant ; 1625.0bp to feature; MODIFIER | silent_mutation | Average:74.249; most accessible tissue: Minghui63 young leaf, score: 85.236 | N | N | N | N |
| vg1000973578 | T -> C | LOC_Os10g02584.1 | downstream_gene_variant ; 2873.0bp to feature; MODIFIER | silent_mutation | Average:74.249; most accessible tissue: Minghui63 young leaf, score: 85.236 | N | N | N | N |
| vg1000973578 | T -> C | LOC_Os10g02584.3 | downstream_gene_variant ; 2873.0bp to feature; MODIFIER | silent_mutation | Average:74.249; most accessible tissue: Minghui63 young leaf, score: 85.236 | N | N | N | N |
| vg1000973578 | T -> C | LOC_Os10g02584.2 | downstream_gene_variant ; 2873.0bp to feature; MODIFIER | silent_mutation | Average:74.249; most accessible tissue: Minghui63 young leaf, score: 85.236 | N | N | N | N |
| vg1000973578 | T -> C | LOC_Os10g02570-LOC_Os10g02584 | intergenic_region ; MODIFIER | silent_mutation | Average:74.249; most accessible tissue: Minghui63 young leaf, score: 85.236 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000973578 | 3.59E-06 | NA | mr1310_2 | 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 |
| vg1000973578 | 5.25E-06 | 3.32E-07 | mr1959_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 |
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