Variant ID: vg0408266266 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 8266266 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 120. )
AGCCTTCTCGGCGAGGTCAACCGAGTTTTGGCACGGTTGATAACCAGAGGAGATGTGATGCTGTGATTGCGGGGCTCAGTAGCGTGTTCGTTCAAAAGCC[G/A]
GATCGAGTTGTGTCACGACTCCGCCCAAATCGACTGTTTATCAATACCTATCGGAACATCGGGACCTATTCCCCATCACAATGACTCATTCATTTTGTTT
AAACAAAATGAATGAGTCATTGTGATGGGGAATAGGTCCCGATGTTCCGATAGGTATTGATAAACAGTCGATTTGGGCGGAGTCGTGACACAACTCGATC[C/T]
GGCTTTTGAACGAACACGCTACTGAGCCCCGCAATCACAGCATCACATCTCCTCTGGTTATCAACCGTGCCAAAACTCGGTTGACCTCGCCGAGAAGGCT
Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 76.20% | 23.70% | 0.06% | 0.00% | NA |
All Indica | 2759 | 94.00% | 5.90% | 0.07% | 0.00% | NA |
All Japonica | 1512 | 38.20% | 61.80% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.70% | 0.20% | 0.17% | 0.00% | NA |
Indica II | 465 | 76.80% | 23.20% | 0.00% | 0.00% | NA |
Indica III | 913 | 97.00% | 3.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 96.30% | 3.60% | 0.13% | 0.00% | NA |
Temperate Japonica | 767 | 4.20% | 95.80% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 93.50% | 6.50% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 31.10% | 68.90% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 74.40% | 24.40% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0408266266 | G -> A | LOC_Os04g14710.1 | intron_variant ; MODIFIER | silent_mutation | Average:31.607; most accessible tissue: Callus, score: 58.332 | N | N | N | N |
vg0408266266 | G -> A | LOC_Os04g14710.2 | intron_variant ; MODIFIER | silent_mutation | Average:31.607; most accessible tissue: Callus, score: 58.332 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0408266266 | NA | 4.84E-07 | mr1715 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0408266266 | NA | 8.21E-07 | mr1739 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0408266266 | NA | 7.26E-07 | mr1826 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0408266266 | NA | 3.90E-09 | mr1959 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0408266266 | NA | 1.30E-07 | mr1993 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0408266266 | NA | 7.86E-12 | mr1378_2 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0408266266 | NA | 8.02E-16 | mr1520_2 | 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 |