Variant ID: vg1121758646 (JBrowse) | Variation Type: SNP |
Chromosome: chr11 | Position: 21758646 |
Reference Allele: G | Alternative Allele: C |
Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 107. )
TGGGCGAAAGTCAGTTAGTTGATTCGGGTCCTCTTTCTTGGACAGGAGGATGATGGAAGCTGTGTTGACGAGATGCAGGTGCTGGGAATTCACTCTCCAG[G/C]
CTAAGTTAAGGGCCGCAACCAAGTCATCTTTGATAATTCCCCAACAAACCTTGAAAAAGGTGGCGCTAAAACCATCTGGCTCTGGCGCCTTGTCACTTGG
CCAAGTGACAAGGCGCCAGAGCCAGATGGTTTTAGCGCCACCTTTTTCAAGGTTTGTTGGGGAATTATCAAAGATGACTTGGTTGCGGCCCTTAACTTAG[C/G]
CTGGAGAGTGAATTCCCAGCACCTGCATCTCGTCAACACAGCTTCCATCATCCTCCTGTCCAAGAAAGAGGACCCGAATCAACTAACTGACTTTCGCCCA
Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 41.30% | 37.50% | 3.83% | 17.39% | NA |
All Indica | 2759 | 25.70% | 59.60% | 4.28% | 10.40% | NA |
All Japonica | 1512 | 65.40% | 2.20% | 1.85% | 30.56% | NA |
Aus | 269 | 77.30% | 16.70% | 3.35% | 2.60% | NA |
Indica I | 595 | 7.90% | 79.50% | 6.22% | 6.39% | NA |
Indica II | 465 | 14.60% | 71.60% | 4.09% | 9.68% | NA |
Indica III | 913 | 42.40% | 40.10% | 2.19% | 15.33% | NA |
Indica Intermediate | 786 | 26.30% | 60.20% | 5.34% | 8.14% | NA |
Temperate Japonica | 767 | 76.90% | 2.30% | 2.09% | 18.64% | NA |
Tropical Japonica | 504 | 53.40% | 2.00% | 1.19% | 43.45% | NA |
Japonica Intermediate | 241 | 53.90% | 2.10% | 2.49% | 41.49% | NA |
VI/Aromatic | 96 | 15.60% | 17.70% | 23.96% | 42.71% | NA |
Intermediate | 90 | 32.20% | 36.70% | 3.33% | 27.78% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1121758646 | G -> DEL | LOC_Os11g36880.1 | N | frameshift_variant | Average:34.823; most accessible tissue: Minghui63 root, score: 45.031 | N | N | N | N |
vg1121758646 | G -> C | LOC_Os11g36880.1 | missense_variant ; p.Ala377Gly; MODERATE | nonsynonymous_codon ; A377G | Average:34.823; most accessible tissue: Minghui63 root, score: 45.031 | unknown | unknown | DELETERIOUS | 0.02 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1121758646 | 9.27E-06 | 9.27E-06 | mr1249 | Ind_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 |
vg1121758646 | NA | 7.58E-06 | mr1283_2 | Ind_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 |
vg1121758646 | NA | 1.88E-07 | mr1624_2 | Ind_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 |
vg1121758646 | NA | 3.13E-08 | mr1740_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 |
vg1121758646 | NA | 8.08E-06 | mr1849_2 | Ind_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 |
vg1121758646 | NA | 4.07E-06 | mr1873_2 | Ind_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 |
vg1121758646 | NA | 1.85E-06 | mr1908_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 |
vg1121758646 | NA | 1.35E-06 | mr1924_2 | Ind_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 |
vg1121758646 | NA | 1.53E-06 | mr1943_2 | Ind_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 |