Search for Variation information by Variation ID:
Detailed information for vg1008324314:
| Variant ID: vg1008324314 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr10 | Position: 8324314 |
| Reference Allele: C | Alternative Allele: G,CTCCAAAGACACG |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 272. )
Flanking Sequence (100 bp) in Reference Genome:
TTCCACGCCATAAACCAGAAAGAATGGCGACTGACCGGTAGCCCGACTGGGAGTAGTACGCAAGGACCAAAGTACAGATGGTAGCTGATCCACCCATTTG[C/G,CTCCAAAGACACG]
CAGCGTAGGGGCGCAATTGGTCAAAAACTCGGGCTTTTATTCCCTGAAGTACCATACCATTAGCGCGTTCAACTTGTCCATTGCTCATGGGGTGTGCTAC
Reverse complement sequence
GTAGCACACCCCATGAGCAATGGACAAGTTGAACGCGCTAATGGTATGGTACTTCAGGGAATAAAAGCCCGAGTTTTTGACCAATTGCGCCCCTACGCTG[G/C,CGTGTCTTTGGAG]
CAAATGGGTGGATCAGCTACCATCTGTACTTTGGTCCTTGCGTACTACTCCCAGTCGGGCTACCGGTCAGTCGCCATTCTTTCTGGTTTATGGCGTGGAA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.60% | 0.40% | 1.46% | 0.47% | CTCCAAAGACACG: 0.04% |
| All Indica | 2759 | 98.50% | 0.70% | 0.80% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.07% | 0.20% | NA |
| Aus | 269 | 75.50% | 0.00% | 17.10% | 6.69% | CTCCAAAGACACG: 0.74% |
| Indica I | 595 | 95.00% | 2.40% | 2.69% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.60% | 0.80% | 0.64% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.20% | 0.60% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 0.00% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1008324314 | C -> CTCCAAAGACACG | LOC_Os10g16700.1 | inframe_insertion ; p.Gly118delinsAlaCysLeuTrpSer; MODERATE | inframe_variant | Average:56.555; most accessible tissue: Zhenshan97 young leaf, score: 80.589 | N | N | N | N |
| vg1008324314 | C -> G | LOC_Os10g16700.1 | missense_variant ; p.Gly118Ala; MODERATE | nonsynonymous_codon ; G118A | Average:56.555; most accessible tissue: Zhenshan97 young leaf, score: 80.589 | benign  |
0.805 |
DELETERIOUS | 0.02 |
| vg1008324314 | C -> DEL | LOC_Os10g16700.1 | N | frameshift_variant | Average:56.555; most accessible tissue: Zhenshan97 young leaf, score: 80.589 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1008324314 | NA | 1.96E-06 | mr1070 | 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 |
| vg1008324314 | 2.36E-06 | NA | mr1128 | 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 |
| vg1008324314 | 3.03E-07 | 4.07E-08 | mr1128 | 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 |
| vg1008324314 | NA | 3.33E-06 | mr1180 | 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 |
| vg1008324314 | NA | 4.77E-06 | mr1053_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 |
| vg1008324314 | NA | 3.23E-07 | mr1128_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 |