Variant ID: vg0618322026 (JBrowse) | Variation Type: SNP |
Chromosome: chr06 | Position: 18322026 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ACGCCGAGTTCTCCTACAATAACAGCTACCAAGCCAGCATACAAATGGCACCCTATGAAGCGTTGTATGGACACAAATGCCGGACACCGCTATTGTGGGA[C/T]
CAAGTTGGGGAAAGCCAAGTGTTCAGGACCGATATCTTGAGAGAAGCTGAAGCGAAGGTCAGAACCATTCAGGATAATCTAAAGGTGGCACAGTCCCAGC
GCTGGGACTGTGCCACCTTTAGATTATCCTGAATGGTTCTGACCTTCGCTTCAGCTTCTCTCAAGATATCGGTCCTGAACACTTGGCTTTCCCCAACTTG[G/A]
TCCCACAATAGCGGTGTCCGGCATTTGTGTCCATACAACGCTTCATAGGGTGCCATTTGTATGCTGGCTTGGTAGCTGTTATTGTAGGAGAACTCGGCGT
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 | 61.60% | 3.40% | 1.95% | 32.97% | NA |
All Indica | 2759 | 52.60% | 4.90% | 2.39% | 40.09% | NA |
All Japonica | 1512 | 82.60% | 0.00% | 0.26% | 17.13% | NA |
Aus | 269 | 46.10% | 9.30% | 7.06% | 37.55% | NA |
Indica I | 595 | 53.80% | 16.10% | 2.86% | 27.23% | NA |
Indica II | 465 | 67.30% | 0.20% | 1.08% | 31.40% | NA |
Indica III | 913 | 41.50% | 0.30% | 2.30% | 55.86% | NA |
Indica Intermediate | 786 | 56.00% | 4.50% | 2.93% | 36.64% | NA |
Temperate Japonica | 767 | 76.70% | 0.00% | 0.13% | 23.21% | NA |
Tropical Japonica | 504 | 91.90% | 0.00% | 0.20% | 7.94% | NA |
Japonica Intermediate | 241 | 82.20% | 0.00% | 0.83% | 17.01% | NA |
VI/Aromatic | 96 | 30.20% | 1.00% | 2.08% | 66.67% | NA |
Intermediate | 90 | 65.60% | 2.20% | 1.11% | 31.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0618322026 | C -> T | LOC_Os06g31480.1 | synonymous_variant ; p.Asp1531Asp; LOW | synonymous_codon | Average:8.731; most accessible tissue: Callus, score: 28.865 | N | N | N | N |
vg0618322026 | C -> DEL | LOC_Os06g31480.1 | N | frameshift_variant | Average:8.731; most accessible tissue: Callus, score: 28.865 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0618322026 | 3.66E-06 | NA | mr1435 | 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 |