Variant ID: vg0321930604 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 21930604 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCGCAGGTTTGCTGCAGCCTTTAAAGATACCAGAATGGAAGTGGGAGGAAATTGGGATGGATTTCATCACTGGTCTGCCCAGAATGTCATCTGGCCATGA[T/C]
TCTATTTGGGTGATAGTCGACAGGCTTACAAAAGTTGCTCATTGCATCCCTGTGAGGACAACATATTCCGGAAATCGTTTGGCAGAATTGTATATGGCAA
TTGCCATATACAATTCTGCCAAACGATTTCCGGAATATGTTGTCCTCACAGGGATGCAATGAGCAACTTTTGTAAGCCTGTCGACTATCACCCAAATAGA[A/G]
TCATGGCCAGATGACATTCTGGGCAGACCAGTGATGAAATCCATCCCAATTTCCTCCCACTTCCATTCTGGTATCTTTAAAGGCTGCAGCAAACCTGCGG
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 | 88.60% | 0.00% | 2.60% | 8.80% | NA |
All Indica | 2759 | 82.00% | 0.10% | 4.13% | 13.77% | NA |
All Japonica | 1512 | 99.00% | 0.00% | 0.07% | 0.93% | NA |
Aus | 269 | 93.70% | 0.00% | 2.23% | 4.09% | NA |
Indica I | 595 | 78.30% | 0.00% | 5.88% | 15.80% | NA |
Indica II | 465 | 72.00% | 0.20% | 4.73% | 23.01% | NA |
Indica III | 913 | 90.30% | 0.10% | 1.75% | 7.89% | NA |
Indica Intermediate | 786 | 81.20% | 0.00% | 5.22% | 13.61% | NA |
Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
Tropical Japonica | 504 | 97.40% | 0.00% | 0.20% | 2.38% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
Intermediate | 90 | 86.70% | 0.00% | 2.22% | 11.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0321930604 | T -> C | LOC_Os03g39460.1 | upstream_gene_variant ; 2129.0bp to feature; MODIFIER | silent_mutation | Average:21.26; most accessible tissue: Zhenshan97 root, score: 32.766 | N | N | N | N |
vg0321930604 | T -> C | LOC_Os03g39490.1 | upstream_gene_variant ; 3111.0bp to feature; MODIFIER | silent_mutation | Average:21.26; most accessible tissue: Zhenshan97 root, score: 32.766 | N | N | N | N |
vg0321930604 | T -> C | LOC_Os03g39450.1 | downstream_gene_variant ; 3647.0bp to feature; MODIFIER | silent_mutation | Average:21.26; most accessible tissue: Zhenshan97 root, score: 32.766 | N | N | N | N |
vg0321930604 | T -> C | LOC_Os03g39460-LOC_Os03g39490 | intergenic_region ; MODIFIER | silent_mutation | Average:21.26; most accessible tissue: Zhenshan97 root, score: 32.766 | N | N | N | N |
vg0321930604 | T -> DEL | N | N | silent_mutation | Average:21.26; most accessible tissue: Zhenshan97 root, score: 32.766 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0321930604 | 3.62E-06 | NA | mr1095_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 |
vg0321930604 | 7.65E-06 | 5.55E-06 | mr1098_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 |
vg0321930604 | 5.68E-06 | NA | mr1563_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 |