Variant ID: vg0817970097 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 17970097 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTTCGCGTTTATCCTAATACATCTTTTTGTATGTTGCAGAAAAGACGTTGTCGTCATCGTCTCTCAAGCCAGAGTGGTAGCTAGCCCTCGAAGGAATTCA[C/T]
GCAGGCAAGTGATGTAAATATATGATTGTTAGATTTTTAATGCAATTAAGACTATTAGATTTAATATACGACACTTAGACTTAGCATTATAATTAGAGTT
AACTCTAATTATAATGCTAAGTCTAAGTGTCGTATATTAAATCTAATAGTCTTAATTGCATTAAAAATCTAACAATCATATATTTACATCACTTGCCTGC[G/A]
TGAATTCCTTCGAGGGCTAGCTACCACTCTGGCTTGAGAGACGATGACGACAACGTCTTTTCTGCAACATACAAAAAGATGTATTAGGATAAACGCGAAG
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 | 92.60% | 0.80% | 0.49% | 6.14% | NA |
All Indica | 2759 | 88.30% | 0.70% | 0.83% | 10.22% | NA |
All Japonica | 1512 | 99.70% | 0.00% | 0.00% | 0.33% | NA |
Aus | 269 | 92.60% | 7.40% | 0.00% | 0.00% | NA |
Indica I | 595 | 91.80% | 2.50% | 0.67% | 5.04% | NA |
Indica II | 465 | 98.50% | 0.00% | 0.00% | 1.51% | NA |
Indica III | 913 | 84.60% | 0.00% | 1.64% | 13.80% | NA |
Indica Intermediate | 786 | 84.00% | 0.40% | 0.51% | 15.14% | NA |
Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
Intermediate | 90 | 98.90% | 0.00% | 0.00% | 1.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0817970097 | C -> T | LOC_Os08g29290.1 | intron_variant ; MODIFIER | silent_mutation | Average:21.419; most accessible tissue: Zhenshan97 flag leaf, score: 31.305 | N | N | N | N |
vg0817970097 | C -> DEL | N | N | silent_mutation | Average:21.419; most accessible tissue: Zhenshan97 flag leaf, score: 31.305 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0817970097 | 2.12E-08 | 2.12E-08 | mr1240 | 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 |