| Variant ID: vg1000604296 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 604296 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.03, others allele: 0.00, population size: 76. )
TGGTAGCAACCTGATCCTGCGTTAGCCGATTCGCAACCTGCCCACTATGCTGTGGGTTCTCTCTCATCAACTGCCGAGGATTAACCAGCTGACCTGGTGC[C/T]
GACATTGACGGAGTAGATGGGGAAATCGATACCGGCGCCGTCGGCTAGGCTGATGATGCAATGGGAGGAACCGCTTGAATAGGTGGATGAATATCGGTGA
TCACCGATATTCATCCACCTATTCAAGCGGTTCCTCCCATTGCATCATCAGCCTAGCCGACGGCGCCGGTATCGATTTCCCCATCTACTCCGTCAATGTC[G/A]
GCACCAGGTCAGCTGGTTAATCCTCGGCAGTTGATGAGAGAGAACCCACAGCATAGTGGGCAGGTTGCGAATCGGCTAACGCAGGATCAGGTTGCTACCA
| 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 | 58.80% | 38.10% | 1.63% | 1.42% | NA |
| All Indica | 2759 | 42.30% | 56.30% | 1.34% | 0.07% | NA |
| All Japonica | 1512 | 93.70% | 2.70% | 0.46% | 3.17% | NA |
| Aus | 269 | 47.20% | 49.10% | 3.72% | 0.00% | NA |
| Indica I | 595 | 38.20% | 61.70% | 0.17% | 0.00% | NA |
| Indica II | 465 | 44.70% | 55.30% | 0.00% | 0.00% | NA |
| Indica III | 913 | 47.50% | 49.20% | 3.07% | 0.22% | NA |
| Indica Intermediate | 786 | 37.80% | 61.20% | 1.02% | 0.00% | NA |
| Temperate Japonica | 767 | 93.50% | 0.70% | 0.26% | 5.61% | NA |
| Tropical Japonica | 504 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 85.90% | 10.00% | 2.07% | 2.07% | NA |
| VI/Aromatic | 96 | 11.50% | 52.10% | 20.83% | 15.62% | NA |
| Intermediate | 90 | 67.80% | 26.70% | 3.33% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000604296 | C -> T | LOC_Os10g01960.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:57.305; most accessible tissue: Minghui63 flag leaf, score: 77.153 | N | N | N | N |
| vg1000604296 | C -> T | LOC_Os10g01950.1 | upstream_gene_variant ; 2386.0bp to feature; MODIFIER | silent_mutation | Average:57.305; most accessible tissue: Minghui63 flag leaf, score: 77.153 | N | N | N | N |
| vg1000604296 | C -> T | LOC_Os10g01970.1 | downstream_gene_variant ; 2845.0bp to feature; MODIFIER | silent_mutation | Average:57.305; most accessible tissue: Minghui63 flag leaf, score: 77.153 | N | N | N | N |
| vg1000604296 | C -> DEL | N | N | silent_mutation | Average:57.305; most accessible tissue: Minghui63 flag leaf, score: 77.153 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000604296 | 3.92E-06 | NA | mr1549 | 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 |
| vg1000604296 | NA | 8.54E-08 | mr1757 | 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 |
| vg1000604296 | NA | 6.84E-06 | mr1549_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 |
| vg1000604296 | NA | 5.21E-06 | mr1757_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 |