Variant ID: vg1121848527 (JBrowse) | Variation Type: SNP |
Chromosome: chr11 | Position: 21848527 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTTCGGGCACGGGCATCGGAACACCTCCCCTCAAATTTAAAATATCCGACGATGGGTAAAACTTGGGGTTTTACAAAAGACTTGGAAAACCCAACACCTG[G/A]
GTCGGTGCTTGTGAACTAAATGAATTTCCAAAACCGCAGACCGGGGGACGAACCGGGAGTACGGTTTCCCGCTCTTGCACTTAAGGACCGTTTCCCTTGG
CCAAGGGAAACGGTCCTTAAGTGCAAGAGCGGGAAACCGTACTCCCGGTTCGTCCCCCGGTCTGCGGTTTTGGAAATTCATTTAGTTCACAAGCACCGAC[C/T]
CAGGTGTTGGGTTTTCCAAGTCTTTTGTAAAACCCCAAGTTTTACCCATCGTCGGATATTTTAAATTTGAGGGGAGGTGTTCCGATGCCCGTGCCCGAAG
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 | 27.80% | 0.20% | 14.73% | 57.24% | NA |
All Indica | 2759 | 16.70% | 0.30% | 17.62% | 65.42% | NA |
All Japonica | 1512 | 41.70% | 0.00% | 10.38% | 47.95% | NA |
Aus | 269 | 64.70% | 0.00% | 11.52% | 23.79% | NA |
Indica I | 595 | 13.40% | 0.00% | 9.58% | 76.97% | NA |
Indica II | 465 | 10.30% | 0.20% | 16.34% | 73.12% | NA |
Indica III | 913 | 22.70% | 0.70% | 22.89% | 53.78% | NA |
Indica Intermediate | 786 | 15.90% | 0.10% | 18.32% | 65.65% | NA |
Temperate Japonica | 767 | 70.80% | 0.00% | 2.48% | 26.73% | NA |
Tropical Japonica | 504 | 6.70% | 0.00% | 21.63% | 71.63% | NA |
Japonica Intermediate | 241 | 22.00% | 0.00% | 12.03% | 65.98% | NA |
VI/Aromatic | 96 | 30.20% | 1.00% | 9.38% | 59.38% | NA |
Intermediate | 90 | 24.40% | 1.10% | 14.44% | 60.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1121848527 | G -> A | LOC_Os11g37010.1 | upstream_gene_variant ; 1708.0bp to feature; MODIFIER | silent_mutation | Average:7.256; most accessible tissue: Callus, score: 22.8 | N | N | N | N |
vg1121848527 | G -> A | LOC_Os11g37000.1 | downstream_gene_variant ; 4987.0bp to feature; MODIFIER | silent_mutation | Average:7.256; most accessible tissue: Callus, score: 22.8 | N | N | N | N |
vg1121848527 | G -> A | LOC_Os11g37020.1 | downstream_gene_variant ; 4845.0bp to feature; MODIFIER | silent_mutation | Average:7.256; most accessible tissue: Callus, score: 22.8 | N | N | N | N |
vg1121848527 | G -> A | LOC_Os11g37000-LOC_Os11g37010 | intergenic_region ; MODIFIER | silent_mutation | Average:7.256; most accessible tissue: Callus, score: 22.8 | N | N | N | N |
vg1121848527 | G -> DEL | N | N | silent_mutation | Average:7.256; most accessible tissue: Callus, score: 22.8 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1121848527 | 4.87E-06 | NA | mr1902_2 | 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 |