Variant ID: vg0113613619 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 13613619 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GACCCCGTCAGCCTGGTATTGATATTGACGTATTTCTTGAACCATTGTTGGAAGATATGGCTGATTTATGGAAAGAGGGATTGAAAATGTGGGACGAGTA[C/T]
TTAAGAGAATACTTCACAGTGAAGGCCATCATCTTCGTGACCATTAACGATTATCCAGCAATGTTTTCAGTTTCAGGTCAAATTAAAGGTAAAAACAGGA
TCCTGTTTTTACCTTTAATTTGACCTGAAACTGAAAACATTGCTGGATAATCGTTAATGGTCACGAAGATGATGGCCTTCACTGTGAAGTATTCTCTTAA[G/A]
TACTCGTCCCACATTTTCAATCCCTCTTTCCATAAATCAGCCATATCTTCCAACAATGGTTCAAGAAATACGTCAATATCAATACCAGGCTGACGGGGTC
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 | 54.00% | 0.80% | 7.70% | 37.54% | NA |
All Indica | 2759 | 39.20% | 0.70% | 9.53% | 50.63% | NA |
All Japonica | 1512 | 87.50% | 0.20% | 2.58% | 9.72% | NA |
Aus | 269 | 20.80% | 0.40% | 13.38% | 65.43% | NA |
Indica I | 595 | 58.80% | 0.30% | 3.19% | 37.65% | NA |
Indica II | 465 | 26.90% | 0.00% | 7.31% | 65.81% | NA |
Indica III | 913 | 33.10% | 1.50% | 14.57% | 50.82% | NA |
Indica Intermediate | 786 | 38.70% | 0.30% | 9.80% | 51.27% | NA |
Temperate Japonica | 767 | 98.80% | 0.00% | 0.26% | 0.91% | NA |
Tropical Japonica | 504 | 67.50% | 0.60% | 6.75% | 25.20% | NA |
Japonica Intermediate | 241 | 93.40% | 0.00% | 1.24% | 5.39% | NA |
VI/Aromatic | 96 | 39.60% | 15.60% | 20.83% | 23.96% | NA |
Intermediate | 90 | 57.80% | 1.10% | 6.67% | 34.44% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0113613619 | C -> T | LOC_Os01g24140.1 | synonymous_variant ; p.Tyr377Tyr; LOW | synonymous_codon | Average:21.738; most accessible tissue: Zhenshan97 root, score: 53.045 | N | N | N | N |
vg0113613619 | C -> DEL | LOC_Os01g24140.1 | N | frameshift_variant | Average:21.738; most accessible tissue: Zhenshan97 root, score: 53.045 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0113613619 | 1.15E-07 | NA | mr1168 | 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 |
vg0113613619 | 9.43E-10 | NA | mr1383 | 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 |
vg0113613619 | 1.05E-07 | 2.04E-06 | mr1383 | 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 |