Variant ID: vg1125474766 (JBrowse) | Variation Type: SNP |
Chromosome: chr11 | Position: 25474766 |
Reference Allele: G | Alternative Allele: C |
Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GAGCACCTTGGCGTTGGTGAAGTTGTGGATGAAATGCGAGTAGTCGACGCATCGCCCCATGCCATGGGTGAAGTGGAGGTCGGCGGCGACCACCGTCGTC[G/C]
TGTCCGGCGACGGCGGCGAGGTTAGGTCGAACAGCACCGCTTCTCCCTTGTACGTGAAGGATCGCAGCCTCAGCGCGGTGATCTCCATTGATCTGCCCGG
CCGGGCAGATCAATGGAGATCACCGCGCTGAGGCTGCGATCCTTCACGTACAAGGGAGAAGCGGTGCTGTTCGACCTAACCTCGCCGCCGTCGCCGGACA[C/G]
GACGACGGTGGTCGCCGCCGACCTCCACTTCACCCATGGCATGGGGCGATGCGTCGACTACTCGCATTTCATCCACAACTTCACCAACGCCAAGGTGCTC
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 | 96.80% | 2.90% | 0.28% | 0.00% | NA |
All Indica | 2759 | 99.00% | 0.90% | 0.04% | 0.00% | NA |
All Japonica | 1512 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
Aus | 269 | 79.60% | 16.40% | 4.09% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.10% | 0.60% | 0.22% | 0.00% | NA |
Indica III | 913 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 52.10% | 47.90% | 0.00% | 0.00% | NA |
Intermediate | 90 | 93.30% | 5.60% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg1125474766 | G -> C | LOC_Os11g42300.1 | missense_variant ; p.Thr289Arg; MODERATE | nonsynonymous_codon ; T289R | Average:72.081; most accessible tissue: Minghui63 panicle, score: 82.128 | unknown | unknown | TOLERATED | 0.54 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1125474766 | 4.86E-09 | NA | mr1191 | 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 |
vg1125474766 | 2.08E-08 | 7.91E-10 | mr1644 | 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 |
vg1125474766 | 2.18E-11 | NA | mr1191_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 |
vg1125474766 | NA | 2.41E-06 | mr1465_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 |
vg1125474766 | NA | 5.43E-06 | mr1522_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 |
vg1125474766 | NA | 2.76E-08 | mr1567_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 |
vg1125474766 | 3.45E-07 | 2.62E-11 | mr1662_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 |