| Variant ID: vg1117172234 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17172234 |
| Reference Allele: C | Alternative Allele: T,A |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.03, others allele: 0.00, population size: 86. )
GGTAAATTTTTACCTACAGTTCTCTCTGTCTATCACTCACCTGATTGGTGGGTTGATACTGGTGCTAATATTCATGTGTGTGCCGACATTTCCCTATTTT[C/T,A]
TTCTTATCAGGTCGGGAGAGGTTCCTCCTTGTTGATGGGAAATAGATCGCTTGCGGCTGTTCATGGTGTTGGTACGGTCGATCTGAAGTTTACTTCGAGA
TCTCGAAGTAAACTTCAGATCGACCGTACCAACACCATGAACAGCCGCAAGCGATCTATTTCCCATCAACAAGGAGGAACCTCTCCCGACCTGATAAGAA[G/A,T]
AAAATAGGGAAATGTCGGCACACACATGAATATTAGCACCAGTATCAACCCACCAATCAGGTGAGTGATAGACAGAGAGAACTGTAGGTAAAAATTTACC
| 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 | 81.00% | 6.10% | 10.94% | 1.95% | A: 0.02% |
| All Indica | 2759 | 70.80% | 8.10% | 17.98% | 3.12% | A: 0.04% |
| All Japonica | 1512 | 95.40% | 4.10% | 0.26% | 0.26% | NA |
| Aus | 269 | 97.40% | 0.00% | 1.86% | 0.74% | NA |
| Indica I | 595 | 60.50% | 1.80% | 30.59% | 7.06% | NA |
| Indica II | 465 | 77.00% | 6.00% | 15.05% | 1.94% | NA |
| Indica III | 913 | 72.70% | 13.80% | 11.83% | 1.53% | A: 0.11% |
| Indica Intermediate | 786 | 72.50% | 7.50% | 17.30% | 2.67% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.13% | 0.39% | NA |
| Tropical Japonica | 504 | 87.50% | 11.90% | 0.40% | 0.20% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.80% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 2.20% | 12.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117172234 | C -> T | LOC_Os11g29600.1 | upstream_gene_variant ; 2877.0bp to feature; MODIFIER | silent_mutation | Average:28.398; most accessible tissue: Minghui63 young leaf, score: 43.347 | N | N | N | N |
| vg1117172234 | C -> T | LOC_Os11g29610.1 | intron_variant ; MODIFIER | silent_mutation | Average:28.398; most accessible tissue: Minghui63 young leaf, score: 43.347 | N | N | N | N |
| vg1117172234 | C -> A | LOC_Os11g29600.1 | upstream_gene_variant ; 2877.0bp to feature; MODIFIER | silent_mutation | Average:28.398; most accessible tissue: Minghui63 young leaf, score: 43.347 | N | N | N | N |
| vg1117172234 | C -> A | LOC_Os11g29610.1 | intron_variant ; MODIFIER | silent_mutation | Average:28.398; most accessible tissue: Minghui63 young leaf, score: 43.347 | N | N | N | N |
| vg1117172234 | C -> DEL | N | N | silent_mutation | Average:28.398; most accessible tissue: Minghui63 young leaf, score: 43.347 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1117172234 | 5.77E-07 | 5.76E-07 | mr1068 | 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 |
| vg1117172234 | NA | 1.48E-07 | mr1090 | 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 |
| vg1117172234 | NA | 7.97E-06 | mr1230 | 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 |
| vg1117172234 | 1.75E-07 | 1.75E-07 | mr1230 | 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 |
| vg1117172234 | 7.96E-06 | 7.95E-06 | mr1391 | 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 |
| vg1117172234 | NA | 3.16E-06 | mr1807 | 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 |
| vg1117172234 | 6.29E-06 | 6.29E-06 | mr1996 | 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 |
| vg1117172234 | NA | 2.64E-06 | mr1068_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 |
| vg1117172234 | NA | 9.83E-06 | mr1078_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 |
| vg1117172234 | NA | 1.56E-08 | mr1090_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 |
| vg1117172234 | NA | 9.96E-07 | mr1211_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 |