Variant ID: vg0815655974 (JBrowse) | Variation Type: INDEL |
Chromosome: chr08 | Position: 15655974 |
Reference Allele: CGCAGTT | Alternative Allele: TGCAGTT,C |
Primary Allele: CGCAGTT | Secondary Allele: TGCAGTT |
Inferred Ancestral Allele: Not determined.
AAGATAACGAGATAACTATTAAATAACTATTAAAAATAATTTGTAAAACAATTTAGATATGATGTATCTAAATAACTATTAAAAATAATTGGTGCTAGCG[CGCAGTT/TGCAGTT,C]
GCGCGGATCACTCTGCTAGTTTATTTGATAATGATTTTTTTGCCGGATAAATGGGTACCCCGGTACCCATTTCATTAACAAATACACAAGACTTAGGTAT
ATACCTAAGTCTTGTGTATTTGTTAATGAAATGGGTACCGGGGTACCCATTTATCCGGCAAAAAAATCATTATCAAATAAACTAGCAGAGTGATCCGCGC[AACTGCG/AACTGCA,G]
CGCTAGCACCAATTATTTTTAATAGTTATTTAGATACATCATATCTAAATTGTTTTACAAATTATTTTTAATAGTTATTTAATAGTTATCTCGTTATCTT
Populations | Population Size | Frequency of CGCAGTT(primary allele) | Frequency of TGCAGTT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 90.00% | 10.00% | 0.00% | 0.00% | C: 0.02% |
All Indica | 2759 | 98.10% | 1.90% | 0.00% | 0.00% | C: 0.04% |
All Japonica | 1512 | 86.40% | 13.60% | 0.00% | 0.00% | NA |
Aus | 269 | 43.50% | 56.50% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 97.70% | 2.20% | 0.00% | 0.00% | C: 0.11% |
Indica Intermediate | 786 | 95.90% | 4.10% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 66.70% | 33.30% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 85.10% | 14.90% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 55.20% | 44.80% | 0.00% | 0.00% | NA |
Intermediate | 90 | 77.80% | 22.20% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0815655974 | CGCAGTT -> C | LOC_Os08g25720.1 | upstream_gene_variant ; 2518.0bp to feature; MODIFIER | silent_mutation | Average:77.773; most accessible tissue: Callus, score: 92.075 | N | N | N | N |
vg0815655974 | CGCAGTT -> C | LOC_Os08g25710-LOC_Os08g25720 | intergenic_region ; MODIFIER | silent_mutation | Average:77.773; most accessible tissue: Callus, score: 92.075 | N | N | N | N |
vg0815655974 | CGCAGTT -> TGCAGTT | LOC_Os08g25720.1 | upstream_gene_variant ; 2519.0bp to feature; MODIFIER | silent_mutation | Average:77.773; most accessible tissue: Callus, score: 92.075 | N | N | N | N |
vg0815655974 | CGCAGTT -> TGCAGTT | LOC_Os08g25710-LOC_Os08g25720 | intergenic_region ; MODIFIER | silent_mutation | Average:77.773; most accessible tissue: Callus, score: 92.075 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0815655974 | NA | 8.81E-08 | mr1029 | 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 |
vg0815655974 | NA | 3.24E-06 | mr1189 | 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 |
vg0815655974 | NA | 5.97E-08 | mr1530 | 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 |
vg0815655974 | NA | 1.08E-06 | mr1625 | 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 |
vg0815655974 | NA | 8.49E-08 | mr1734 | 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 |
vg0815655974 | NA | 1.42E-11 | mr1047_2 | 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 |
vg0815655974 | NA | 8.00E-06 | mr1200_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 |
vg0815655974 | NA | 8.78E-06 | mr1295_2 | 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 |
vg0815655974 | NA | 6.54E-06 | mr1344_2 | 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 |
vg0815655974 | NA | 6.10E-08 | mr1526_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 |
vg0815655974 | NA | 4.06E-09 | mr1642_2 | 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 |
vg0815655974 | NA | 4.81E-07 | mr1808_2 | 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 |
vg0815655974 | NA | 1.61E-06 | mr1815_2 | 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 |