Search for Variation information by Variation ID:
Detailed information for vg0707879605:
| Variant ID: vg0707879605 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 7879605 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.04, others allele: 0.00, population size: 94. )
Flanking Sequence (100 bp) in Reference Genome:
AGGAGATATGAAAGCGCTATCTGTGATCTCGCCGGGCACGGATCCGAGAAGGAAGACTACCCTGTTGTCGACTACGAGTCAGACCTTCGGACCAACATGT[C/T]
GACAACAGTTAGATAGGCTGCCCACATATTGTACTGGTGTGATTATTGTCACGTCCTGATAAATTCATCCCAAAATAAAAGTCATTTTCAAAAAGGAAAA
Reverse complement sequence
TTTTCCTTTTTGAAAATGACTTTTATTTTGGGATGAATTTATCAGGACGTGACAATAATCACACCAGTACAATATGTGGGCAGCCTATCTAACTGTTGTC[G/A]
ACATGTTGGTCCGAAGGTCTGACTCGTAGTCGACAACAGGGTAGTCTTCCTTCTCGGATCCGTGCCCGGCGAGATCACAGATAGCGCTTTCATATCTCCT
Allele Frequencies:
| 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 | 73.30% | 22.70% | 3.96% | 0.08% | NA |
| All Indica | 2759 | 55.00% | 38.20% | 6.71% | 0.14% | NA |
| All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.90% | 0.70% | 0.37% | 0.00% | NA |
| Indica I | 595 | 22.70% | 60.80% | 15.80% | 0.67% | NA |
| Indica II | 465 | 81.50% | 15.50% | 3.01% | 0.00% | NA |
| Indica III | 913 | 62.50% | 33.30% | 4.16% | 0.00% | NA |
| Indica Intermediate | 786 | 55.00% | 40.10% | 4.96% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 14.40% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0707879605 | C -> DEL | LOC_Os07g13728.1 | N | frameshift_variant | Average:27.721; most accessible tissue: Minghui63 flag leaf, score: 39.69 | N | N | N | N |
| vg0707879605 | C -> T | LOC_Os07g13728.1 | missense_variant ; p.Ser287Leu; MODERATE | nonsynonymous_codon ; S287L | Average:27.721; most accessible tissue: Minghui63 flag leaf, score: 39.69 | benign  |
0.178 |
TOLERATED | 0.06 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0707879605 | NA | 6.50E-06 | mr1519 | 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 |
| vg0707879605 | 4.36E-06 | NA | mr1630 | 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 |
| vg0707879605 | 6.21E-06 | NA | mr1630 | 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 |