Variant ID: vg1221401988 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 21401988 |
Reference Allele: T | Alternative Allele: A |
Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTGCTGGCCTTGGAACTCTTCAAACTCTTCTTCCGCGAAAACGGACTCTCCGGTAACGACGGAATCTAAGCAGAAAAGAGCAAAATCACCAAAACAGCAC[T/A]
TAAACAAACATGAACAGTACATGTGGATATTTTTAATGTGTAGATCTCAATTTTAGAAAAATTTAGAGACTTGAACCAACTAAATCGGAGCTAAGATGAA
TTCATCTTAGCTCCGATTTAGTTGGTTCAAGTCTCTAAATTTTTCTAAAATTGAGATCTACACATTAAAAATATCCACATGTACTGTTCATGTTTGTTTA[A/T]
GTGCTGTTTTGGTGATTTTGCTCTTTTCTGCTTAGATTCCGTCGTTACCGGAGAGTCCGTTTTCGCGGAAGAAGAGTTTGAAGAGTTCCAAGGCCAGCAA
Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 62.10% | 0.30% | 14.90% | 22.73% | NA |
All Indica | 2759 | 54.30% | 0.00% | 19.97% | 25.70% | NA |
All Japonica | 1512 | 84.80% | 0.70% | 6.55% | 8.00% | NA |
Aus | 269 | 14.90% | 0.00% | 10.41% | 74.72% | NA |
Indica I | 595 | 57.10% | 0.00% | 6.89% | 35.97% | NA |
Indica II | 465 | 70.10% | 0.00% | 10.75% | 19.14% | NA |
Indica III | 913 | 39.40% | 0.00% | 35.60% | 24.97% | NA |
Indica Intermediate | 786 | 60.10% | 0.10% | 17.18% | 22.65% | NA |
Temperate Japonica | 767 | 88.00% | 0.40% | 2.87% | 8.74% | NA |
Tropical Japonica | 504 | 79.80% | 1.20% | 12.10% | 6.94% | NA |
Japonica Intermediate | 241 | 85.10% | 0.40% | 6.64% | 7.88% | NA |
VI/Aromatic | 96 | 57.30% | 0.00% | 14.58% | 28.12% | NA |
Intermediate | 90 | 67.80% | 1.10% | 13.33% | 17.78% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1221401988 | T -> DEL | N | N | silent_mutation | Average:39.763; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 | N | N | N | N |
vg1221401988 | T -> A | LOC_Os12g35180.1 | upstream_gene_variant ; 4605.0bp to feature; MODIFIER | silent_mutation | Average:39.763; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 | N | N | N | N |
vg1221401988 | T -> A | LOC_Os12g35239.1 | upstream_gene_variant ; 3839.0bp to feature; MODIFIER | silent_mutation | Average:39.763; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 | N | N | N | N |
vg1221401988 | T -> A | LOC_Os12g35190.1 | downstream_gene_variant ; 1672.0bp to feature; MODIFIER | silent_mutation | Average:39.763; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 | N | N | N | N |
vg1221401988 | T -> A | LOC_Os12g35200.1 | downstream_gene_variant ; 1483.0bp to feature; MODIFIER | silent_mutation | Average:39.763; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 | N | N | N | N |
vg1221401988 | T -> A | LOC_Os12g35190-LOC_Os12g35200 | intergenic_region ; MODIFIER | silent_mutation | Average:39.763; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1221401988 | 1.01E-06 | 3.47E-06 | mr1895 | 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 |