Variant ID: vg0613263498 (JBrowse) | Variation Type: SNP |
Chromosome: chr06 | Position: 13263498 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 232. )
GGCTCGGTACTTGCAAGGGGTGCGCCGTTATCATAATCGCAATGTTCGATCACGAGCTTTTTTAGTCGGCGACCTGGTTCTGAGAAAAATTCAAACTACA[C/T]
AGGATCGGCACAAGTTATCTCCCTTATGGGAAGGACCATTCATAATTTCCAAAGTCACTCGGCCAGGTTCTTACCGACTCAAGCGTGAAGACGGTACTCC
GGAGTACCGTCTTCACGCTTGAGTCGGTAAGAACCTGGCCGAGTGACTTTGGAAATTATGAATGGTCCTTCCCATAAGGGAGATAACTTGTGCCGATCCT[G/A]
TGTAGTTTGAATTTTTCTCAGAACCAGGTCGCCGACTAAAAAAGCTCGTGATCGAACATTGCGATTATGATAACGGCGCACCCCTTGCAAGTACCGAGCC
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 | 50.00% | 49.70% | 0.21% | 0.13% | NA |
All Indica | 2759 | 21.20% | 78.40% | 0.25% | 0.18% | NA |
All Japonica | 1512 | 97.60% | 2.30% | 0.13% | 0.00% | NA |
Aus | 269 | 61.30% | 38.30% | 0.37% | 0.00% | NA |
Indica I | 595 | 19.30% | 80.20% | 0.34% | 0.17% | NA |
Indica II | 465 | 9.90% | 89.70% | 0.22% | 0.22% | NA |
Indica III | 913 | 28.50% | 71.10% | 0.22% | 0.22% | NA |
Indica Intermediate | 786 | 20.90% | 78.80% | 0.25% | 0.13% | NA |
Temperate Japonica | 767 | 96.50% | 3.50% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 98.80% | 1.00% | 0.20% | 0.00% | NA |
Japonica Intermediate | 241 | 98.30% | 1.20% | 0.41% | 0.00% | NA |
VI/Aromatic | 96 | 85.40% | 14.60% | 0.00% | 0.00% | NA |
Intermediate | 90 | 60.00% | 38.90% | 0.00% | 1.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0613263498 | C -> T | LOC_Os06g22770.1 | downstream_gene_variant ; 1222.0bp to feature; MODIFIER | silent_mutation | Average:35.469; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 | N | N | N | N |
vg0613263498 | C -> T | LOC_Os06g22790.1 | downstream_gene_variant ; 476.0bp to feature; MODIFIER | silent_mutation | Average:35.469; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 | N | N | N | N |
vg0613263498 | C -> T | LOC_Os06g22780.1 | intron_variant ; MODIFIER | silent_mutation | Average:35.469; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 | N | N | N | N |
vg0613263498 | C -> DEL | N | N | silent_mutation | Average:35.469; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0613263498 | 3.86E-06 | NA | mr1141_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 |