| Variant ID: vg1205811130 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 5811130 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATTTTGTTCATCTGGCGCACTTGATGTGACAACACGCGCACGCGTGAGCATCATTCACTTTATCTCCGAGAACAGGGCCGAAAGATGATAGTGACAACTC[G/A]
AACTACCAAGGTATATGTGTACTGTGGTCTGCTGCGCTACCTAAATGAGCCAATCTTCACGCGCCGAAAGTTTGTTGTCGTATGCGTAAGTAGTTTTAAT
ATTAAAACTACTTACGCATACGACAACAAACTTTCGGCGCGTGAAGATTGGCTCATTTAGGTAGCGCAGCAGACCACAGTACACATATACCTTGGTAGTT[C/T]
GAGTTGTCACTATCATCTTTCGGCCCTGTTCTCGGAGATAAAGTGAATGATGCTCACGCGTGCGCGTGTTGTCACATCAAGTGCGCCAGATGAACAAAAT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 63.10% | 0.70% | 9.92% | 26.26% | NA |
| All Indica | 2759 | 49.30% | 1.20% | 15.04% | 34.47% | NA |
| All Japonica | 1512 | 93.90% | 0.00% | 1.06% | 5.03% | NA |
| Aus | 269 | 40.50% | 0.00% | 8.92% | 50.56% | NA |
| Indica I | 595 | 11.40% | 2.00% | 9.75% | 76.81% | NA |
| Indica II | 465 | 69.90% | 0.00% | 15.27% | 14.84% | NA |
| Indica III | 913 | 65.20% | 1.50% | 16.87% | 16.43% | NA |
| Indica Intermediate | 786 | 47.30% | 0.90% | 16.79% | 34.99% | NA |
| Temperate Japonica | 767 | 90.50% | 0.00% | 1.56% | 7.95% | NA |
| Tropical Japonica | 504 | 97.40% | 0.00% | 0.40% | 2.18% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.83% | 1.66% | NA |
| VI/Aromatic | 96 | 26.00% | 1.00% | 8.33% | 64.58% | NA |
| Intermediate | 90 | 75.60% | 0.00% | 6.67% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1205811130 | G -> DEL | N | N | silent_mutation | Average:9.343; most accessible tissue: Callus, score: 23.461 | N | N | N | N |
| vg1205811130 | G -> A | LOC_Os12g10784.1 | downstream_gene_variant ; 3892.0bp to feature; MODIFIER | silent_mutation | Average:9.343; most accessible tissue: Callus, score: 23.461 | N | N | N | N |
| vg1205811130 | G -> A | LOC_Os12g10784.2 | downstream_gene_variant ; 3892.0bp to feature; MODIFIER | silent_mutation | Average:9.343; most accessible tissue: Callus, score: 23.461 | N | N | N | N |
| vg1205811130 | G -> A | LOC_Os12g10784.3 | downstream_gene_variant ; 3892.0bp to feature; MODIFIER | silent_mutation | Average:9.343; most accessible tissue: Callus, score: 23.461 | N | N | N | N |
| vg1205811130 | G -> A | LOC_Os12g10800.1 | intron_variant ; MODIFIER | silent_mutation | Average:9.343; most accessible tissue: Callus, score: 23.461 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1205811130 | 6.03E-06 | NA | mr1439 | 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 |
| vg1205811130 | 3.46E-06 | NA | mr1705 | 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 |
| vg1205811130 | 1.21E-06 | NA | mr1803 | 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 |