Variant ID: vg0704371633 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 4371633 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ACACATGCTTCAAGTGGCTAGGAGGACATCCTCCCTTTTAAGGAGGTCCCCCTCTCCTAGAATAAGCAAGGTGGTACTAAACTCCACATGCATGCCATCC[C/T]
ATGAGGTGGGCTTTTGTGATTTTCCAAAGAATTAATCTTCGAGTGGGCTAAGGCCCATTCATTAATTCCAACATTTAGCCCATGAACTTTTGCATATTAC
GTAATATGCAAAAGTTCATGGGCTAAATGTTGGAATTAATGAATGGGCCTTAGCCCACTCGAAGATTAATTCTTTGGAAAATCACAAAAGCCCACCTCAT[G/A]
GGATGGCATGCATGTGGAGTTTAGTACCACCTTGCTTATTCTAGGAGAGGGGGACCTCCTTAAAAGGGAGGATGTCCTCCTAGCCACTTGAAGCATGTGT
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 | 57.50% | 1.80% | 8.23% | 32.48% | NA |
All Indica | 2759 | 32.70% | 0.00% | 13.12% | 54.11% | NA |
All Japonica | 1512 | 93.20% | 5.50% | 0.93% | 0.40% | NA |
Aus | 269 | 89.60% | 0.00% | 2.97% | 7.43% | NA |
Indica I | 595 | 24.90% | 0.00% | 12.10% | 63.03% | NA |
Indica II | 465 | 42.60% | 0.00% | 14.19% | 43.23% | NA |
Indica III | 913 | 29.40% | 0.00% | 11.94% | 58.71% | NA |
Indica Intermediate | 786 | 36.80% | 0.10% | 14.63% | 48.47% | NA |
Temperate Japonica | 767 | 98.60% | 0.30% | 0.91% | 0.26% | NA |
Tropical Japonica | 504 | 92.90% | 6.30% | 0.40% | 0.40% | NA |
Japonica Intermediate | 241 | 76.80% | 20.30% | 2.07% | 0.83% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 75.60% | 1.10% | 5.56% | 17.78% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0704371633 | C -> DEL | N | N | silent_mutation | Average:20.491; most accessible tissue: Minghui63 root, score: 25.504 | N | N | N | N |
vg0704371633 | C -> T | LOC_Os07g08480.1 | downstream_gene_variant ; 2583.0bp to feature; MODIFIER | silent_mutation | Average:20.491; most accessible tissue: Minghui63 root, score: 25.504 | N | N | N | N |
vg0704371633 | C -> T | LOC_Os07g08480-LOC_Os07g08490 | intergenic_region ; MODIFIER | silent_mutation | Average:20.491; most accessible tissue: Minghui63 root, score: 25.504 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0704371633 | 2.15E-07 | 7.59E-11 | mr1350_2 | 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 |