Search for Variation information by Variation ID:
Detailed information for vg0602255305:
| Variant ID: vg0602255305 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 2255305 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, A: 0.00, others allele: 0.00, population size: 318. )
Flanking Sequence (100 bp) in Reference Genome:
CACAAAAGGTAAAACATTTCCGATTATATGAAATGGTATATGATAGCTTACTGGAGGCAAAATCTTAGCACAAAACAAAAAGATAGAGGGATCATACATG[C/A]
TGACCAGCATCCCATAATATCTTATCCATTGGGGCATTGAAGACATAATGTATAGCAATAGCGAGCTCCACAACAGAATGTCCAGTGTTACATGGTTGGC
Reverse complement sequence
GCCAACCATGTAACACTGGACATTCTGTTGTGGAGCTCGCTATTGCTATACATTATGTCTTCAATGCCCCAATGGATAAGATATTATGGGATGCTGGTCA[G/T]
CATGTATGATCCCTCTATCTTTTTGTTTTGTGCTAAGATTTTGCCTCCAGTAAGCTATCATATACCATTTCATATAATCGGAAATGTTTTACCTTTTGTG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.20% | 3.80% | 0.06% | 0.00% | NA |
| All Indica | 2759 | 99.50% | 0.50% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 95.60% | 4.20% | 0.13% | 0.00% | NA |
| Aus | 269 | 68.40% | 31.60% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.10% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 88.10% | 11.70% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 84.40% | 15.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0602255305 | C -> A | LOC_Os06g05100.1 | missense_variant ; p.Gln149His; MODERATE | nonsynonymous_codon ; Q149H | Average:58.603; most accessible tissue: Callus, score: 73.515 | possibly damaging  |
1.846 |
TOLERATED | 1.00 |
| vg0602255305 | C -> A | LOC_Os06g05100.2 | missense_variant ; p.Gln38His; MODERATE | nonsynonymous_codon ; Q38H | Average:58.603; most accessible tissue: Callus, score: 73.515 | possibly damaging |
1.846 |
TOLERATED | 1.00 |
| vg0602255305 | C -> A | LOC_Os06g05100.5 | missense_variant ; p.Gln38His; MODERATE | nonsynonymous_codon ; Q38H | Average:58.603; most accessible tissue: Callus, score: 73.515 | possibly damaging |
1.898 |
TOLERATED | 1.00 |
| vg0602255305 | C -> A | LOC_Os06g05100.4 | missense_variant ; p.Ser16Ile; MODERATE | nonsynonymous_codon ; S16I | Average:58.603; most accessible tissue: Callus, score: 73.515 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0602255305 | C -> A | LOC_Os06g05100.3 | missense_variant ; p.Gln149His; MODERATE | nonsynonymous_codon ; Q149H | Average:58.603; most accessible tissue: Callus, score: 73.515 | possibly damaging |
1.846 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0602255305 | NA | 6.64E-06 | mr1076 | Jap_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 |
| vg0602255305 | NA | 7.13E-06 | mr1082 | Jap_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 |
| vg0602255305 | NA | 3.56E-07 | mr1083 | Jap_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 |
| vg0602255305 | 1.48E-07 | 1.48E-07 | mr1204 | Jap_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 |
| vg0602255305 | NA | 7.02E-07 | mr1226 | Jap_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 |
| vg0602255305 | NA | 3.62E-07 | mr1227 | Jap_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 |
| vg0602255305 | 3.51E-06 | 3.51E-06 | mr1436 | Jap_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 |
| vg0602255305 | 8.98E-06 | 8.98E-06 | mr1076_2 | Jap_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 |