| Variant ID: vg1012224239 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12224239 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GCCGCGGCGAGGATGCCCTGTCTCTATTCGCCAGCATGCAACGAGCCGGCGTGACGCCGAACGAGGTGACCCTCCTCGGCGTCCTCACGGCGTGCTGTCA[T/C]
GCCGGACTCATCGAGGAGGGGCTCCAGCAACTCGACGCCATGAGGAGGAACGAGATCGACAAGGTCCCCGGCTGCAGCCTCATCGAGATCGACGGCGTTG
CAACGCCGTCGATCTCGATGAGGCTGCAGCCGGGGACCTTGTCGATCTCGTTCCTCCTCATGGCGTCGAGTTGCTGGAGCCCCTCCTCGATGAGTCCGGC[A/G]
TGACAGCACGCCGTGAGGACGCCGAGGAGGGTCACCTCGTTCGGCGTCACGCCGGCTCGTTGCATGCTGGCGAATAGAGACAGGGCATCCTCGCCGCGGC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.60% | 0.30% | 1.52% | 49.60% | NA |
| All Indica | 2759 | 31.40% | 0.30% | 2.46% | 65.86% | NA |
| All Japonica | 1512 | 88.40% | 0.10% | 0.07% | 11.38% | NA |
| Aus | 269 | 10.80% | 1.10% | 1.12% | 86.99% | NA |
| Indica I | 595 | 11.30% | 0.50% | 3.03% | 85.21% | NA |
| Indica II | 465 | 40.00% | 0.00% | 2.58% | 57.42% | NA |
| Indica III | 913 | 35.00% | 0.30% | 2.30% | 62.32% | NA |
| Indica Intermediate | 786 | 37.40% | 0.10% | 2.16% | 60.31% | NA |
| Temperate Japonica | 767 | 95.60% | 0.00% | 0.00% | 4.43% | NA |
| Tropical Japonica | 504 | 81.70% | 0.00% | 0.20% | 18.06% | NA |
| Japonica Intermediate | 241 | 79.70% | 0.80% | 0.00% | 19.50% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 0.00% | 90.62% | NA |
| Intermediate | 90 | 62.20% | 0.00% | 0.00% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012224239 | T -> C | LOC_Os10g23830.1 | synonymous_variant ; p.His111His; LOW | synonymous_codon | Average:14.138; most accessible tissue: Callus, score: 56.934 | N | N | N | N |
| vg1012224239 | T -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:14.138; most accessible tissue: Callus, score: 56.934 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1012224239 | NA | 8.45E-06 | mr1157 | 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 |
| vg1012224239 | NA | 1.60E-07 | mr1328 | 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 |
| vg1012224239 | NA | 1.89E-07 | mr1446 | 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 |
| vg1012224239 | NA | 3.07E-06 | mr1654 | 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 |
| vg1012224239 | NA | 2.86E-06 | mr1815 | 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 |
| vg1012224239 | 8.06E-06 | 1.15E-08 | mr1446_2 | 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 |