| Variant ID: vg1009500303 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr10 | Position: 9500303 |
| Reference Allele: GC | Alternative Allele: AC,G |
| Primary Allele: GC | Secondary Allele: AC |
Inferred Ancestral Allele: Not determined.
CTAGGTCCCAAATCCCCTCTCCCACCTTAGTCAAAGGGTGGTCAAAGCCCCCTCCCGCCAGTCAGACCTCGGTCAAACCCACCCATTGACTCCCTCCCCC[GC/AC,G]
CCACCACTTCGTTGTTTACGTCTCGCAGGAATTCCGCAGTAACATAATGGTCATTGTGCAGTAACATGACAATTTTCTTGCAGTAACAACATCGAAAAAT
ATTTTTCGATGTTGTTACTGCAAGAAAATTGTCATGTTACTGCACAATGACCATTATGTTACTGCGGAATTCCTGCGAGACGTAAACAACGAAGTGGTGG[GC/GT,C]
GGGGGAGGGAGTCAATGGGTGGGTTTGACCGAGGTCTGACTGGCGGGAGGGGGCTTTGACCACCCTTTGACTAAGGTGGGAGAGGGGATTTGGGACCTAG
| Populations | Population Size | Frequency of GC(primary allele) | Frequency of AC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.10% | 0.10% | 2.73% | 15.00% | G: 0.02% |
| All Indica | 2759 | 88.00% | 0.10% | 2.61% | 9.31% | NA |
| All Japonica | 1512 | 85.80% | 0.00% | 0.73% | 13.43% | NA |
| Aus | 269 | 3.30% | 1.90% | 16.36% | 78.44% | NA |
| Indica I | 595 | 98.70% | 0.00% | 0.17% | 1.18% | NA |
| Indica II | 465 | 92.00% | 0.00% | 1.51% | 6.45% | NA |
| Indica III | 913 | 80.40% | 0.20% | 4.16% | 15.22% | NA |
| Indica Intermediate | 786 | 86.40% | 0.00% | 3.31% | 10.31% | NA |
| Temperate Japonica | 767 | 87.00% | 0.00% | 0.52% | 12.52% | NA |
| Tropical Japonica | 504 | 91.10% | 0.00% | 0.60% | 8.33% | NA |
| Japonica Intermediate | 241 | 71.40% | 0.00% | 1.66% | 26.97% | NA |
| VI/Aromatic | 96 | 72.90% | 0.00% | 2.08% | 23.96% | G: 1.04% |
| Intermediate | 90 | 83.30% | 0.00% | 0.00% | 16.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1009500303 | GC -> G | LOC_Os10g18700.1 | upstream_gene_variant ; 1494.0bp to feature; MODIFIER | silent_mutation | Average:21.429; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| vg1009500303 | GC -> G | LOC_Os10g18670-LOC_Os10g18700 | intergenic_region ; MODIFIER | silent_mutation | Average:21.429; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| vg1009500303 | GC -> AC | LOC_Os10g18700.1 | upstream_gene_variant ; 1495.0bp to feature; MODIFIER | silent_mutation | Average:21.429; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| vg1009500303 | GC -> AC | LOC_Os10g18670-LOC_Os10g18700 | intergenic_region ; MODIFIER | silent_mutation | Average:21.429; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| vg1009500303 | GC -> DEL | N | N | silent_mutation | Average:21.429; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1009500303 | NA | 7.99E-06 | mr1545 | 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 |
| vg1009500303 | NA | 2.96E-06 | mr1621 | 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 |
| vg1009500303 | 8.71E-06 | 8.71E-06 | mr1986 | 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 |