Variant ID: vg0802790437 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 2790437 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GAAGCATTCTATATAGTTCTTGCAGAAAACTGAATACTTCCCTTTTCTTATAACAGGTGATGCTGTCATACCAAACACACTTGGCTTATGTTCTGATTTG[T/C]
AATAGAACTCCTGAGATTGTGATAAGTTATAACTTATGACAAACACAAAAAAGAAAAACCTGAATGCAAATATTCATGGTAGTGTCAAAACAAAAAAAAA
TTTTTTTTTGTTTTGACACTACCATGAATATTTGCATTCAGGTTTTTCTTTTTTGTGTTTGTCATAAGTTATAACTTATCACAATCTCAGGAGTTCTATT[A/G]
CAAATCAGAACATAAGCCAAGTGTGTTTGGTATGACAGCATCACCTGTTATAAGAAAAGGGAAGTATTCAGTTTTCTGCAAGAACTATATAGAATGCTTC
Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 94.40% | 2.80% | 2.18% | 0.70% | NA |
All Indica | 2759 | 90.80% | 4.50% | 3.52% | 1.16% | NA |
All Japonica | 1512 | 99.70% | 0.10% | 0.26% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 86.70% | 5.40% | 7.90% | 0.00% | NA |
Indica II | 465 | 91.20% | 3.90% | 4.09% | 0.86% | NA |
Indica III | 913 | 94.00% | 3.50% | 0.55% | 1.97% | NA |
Indica Intermediate | 786 | 90.10% | 5.30% | 3.31% | 1.27% | NA |
Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
Tropical Japonica | 504 | 99.40% | 0.00% | 0.60% | 0.00% | NA |
Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
Intermediate | 90 | 92.20% | 4.40% | 2.22% | 1.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0802790437 | T -> C | LOC_Os08g05310.1 | downstream_gene_variant ; 4677.0bp to feature; MODIFIER | silent_mutation | Average:50.441; most accessible tissue: Callus, score: 72.307 | N | N | N | N |
vg0802790437 | T -> C | LOC_Os08g05320.2 | intron_variant ; MODIFIER | silent_mutation | Average:50.441; most accessible tissue: Callus, score: 72.307 | N | N | N | N |
vg0802790437 | T -> C | LOC_Os08g05320.3 | intron_variant ; MODIFIER | silent_mutation | Average:50.441; most accessible tissue: Callus, score: 72.307 | N | N | N | N |
vg0802790437 | T -> DEL | N | N | silent_mutation | Average:50.441; most accessible tissue: Callus, score: 72.307 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0802790437 | 1.31E-06 | NA | mr1308 | 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 |