| Variant ID: vg1001246160 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr10 | Position: 1246160 |
| Reference Allele: C | Alternative Allele: CAA,T |
| Primary Allele: C | Secondary Allele: CAA |
Inferred Ancestral Allele: Not determined.
GACTCACGCTCTCTCTCTATTTATACCCGAGATAGGCAGCCTAAAGCCACGAATCAAACTCATACTAGAAGTCCTAAACACCTTAGAAAACCCTCTAGTA[C/CAA,T]
AAGAAACAAACTTTACATAACCAATCATACCAAATTTGGACTCCTTCCAAATTCGATTCCGCATCCCATACACACACAATACCTCCATCGTATGCCGTAT
ATACGGCATACGATGGAGGTATTGTGTGTGTATGGGATGCGGAATCGAATTTGGAAGGAGTCCAAATTTGGTATGATTGGTTATGTAAAGTTTGTTTCTT[G/TTG,A]
TACTAGAGGGTTTTCTAAGGTGTTTAGGACTTCTAGTATGAGTTTGATTCGTGGCTTTAGGCTGCCTATCTCGGGTATAAATAGAGAGAGAGCGTGAGTC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CAA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 69.40% | 1.50% | 3.41% | 25.69% | T: 0.04% |
| All Indica | 2759 | 67.90% | 2.40% | 4.46% | 25.12% | T: 0.07% |
| All Japonica | 1512 | 73.20% | 0.10% | 2.31% | 24.40% | NA |
| Aus | 269 | 61.30% | 0.40% | 0.37% | 37.92% | NA |
| Indica I | 595 | 42.90% | 1.30% | 8.24% | 47.56% | NA |
| Indica II | 465 | 70.10% | 3.20% | 3.44% | 23.23% | NA |
| Indica III | 913 | 82.90% | 2.80% | 2.19% | 11.83% | T: 0.22% |
| Indica Intermediate | 786 | 68.20% | 2.30% | 4.83% | 24.68% | NA |
| Temperate Japonica | 767 | 79.10% | 0.10% | 2.09% | 18.64% | NA |
| Tropical Japonica | 504 | 69.40% | 0.00% | 2.18% | 28.37% | NA |
| Japonica Intermediate | 241 | 62.20% | 0.00% | 3.32% | 34.44% | NA |
| VI/Aromatic | 96 | 71.90% | 0.00% | 1.04% | 27.08% | NA |
| Intermediate | 90 | 72.20% | 0.00% | 1.11% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1001246160 | C -> CAA | LOC_Os10g02990.1 | upstream_gene_variant ; 501.0bp to feature; MODIFIER | silent_mutation | Average:6.494; most accessible tissue: Callus, score: 13.9 | N | N | N | N |
| vg1001246160 | C -> CAA | LOC_Os10g02980.1 | downstream_gene_variant ; 4389.0bp to feature; MODIFIER | silent_mutation | Average:6.494; most accessible tissue: Callus, score: 13.9 | N | N | N | N |
| vg1001246160 | C -> CAA | LOC_Os10g03000.1 | downstream_gene_variant ; 1757.0bp to feature; MODIFIER | silent_mutation | Average:6.494; most accessible tissue: Callus, score: 13.9 | N | N | N | N |
| vg1001246160 | C -> CAA | LOC_Os10g03010.1 | downstream_gene_variant ; 4541.0bp to feature; MODIFIER | silent_mutation | Average:6.494; most accessible tissue: Callus, score: 13.9 | N | N | N | N |
| vg1001246160 | C -> CAA | LOC_Os10g02990-LOC_Os10g03000 | intergenic_region ; MODIFIER | silent_mutation | Average:6.494; most accessible tissue: Callus, score: 13.9 | N | N | N | N |
| vg1001246160 | C -> T | LOC_Os10g02990.1 | upstream_gene_variant ; 500.0bp to feature; MODIFIER | silent_mutation | Average:6.494; most accessible tissue: Callus, score: 13.9 | N | N | N | N |
| vg1001246160 | C -> T | LOC_Os10g02980.1 | downstream_gene_variant ; 4388.0bp to feature; MODIFIER | silent_mutation | Average:6.494; most accessible tissue: Callus, score: 13.9 | N | N | N | N |
| vg1001246160 | C -> T | LOC_Os10g03000.1 | downstream_gene_variant ; 1758.0bp to feature; MODIFIER | silent_mutation | Average:6.494; most accessible tissue: Callus, score: 13.9 | N | N | N | N |
| vg1001246160 | C -> T | LOC_Os10g03010.1 | downstream_gene_variant ; 4542.0bp to feature; MODIFIER | silent_mutation | Average:6.494; most accessible tissue: Callus, score: 13.9 | N | N | N | N |
| vg1001246160 | C -> T | LOC_Os10g02990-LOC_Os10g03000 | intergenic_region ; MODIFIER | silent_mutation | Average:6.494; most accessible tissue: Callus, score: 13.9 | N | N | N | N |
| vg1001246160 | C -> DEL | N | N | silent_mutation | Average:6.494; most accessible tissue: Callus, score: 13.9 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1001246160 | 7.80E-06 | 7.81E-06 | mr1421 | 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 |
| vg1001246160 | 4.29E-06 | 4.29E-06 | mr1421 | Ind_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 |
| vg1001246160 | 8.64E-06 | 2.56E-06 | mr1469 | 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 |
| vg1001246160 | 1.62E-06 | 1.62E-06 | mr1752 | 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 |
| vg1001246160 | 6.27E-06 | 6.27E-06 | mr1752 | Ind_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 |