Variant ID: vg0724293530 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 24293530 |
Reference Allele: C | Alternative Allele: A,T |
Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGGGAAATGTCTTCACTTTGTCATCCTAGAACTAGAATGGTTCCAAAACGGTTGATAGGTACTCCCTCCGTTTCACAATGTAAGTCATTCTAGCATTTCC[C/A,T]
ACATTCATATTAATGTTAATGAATCTAGACATATATATCTATCTAGATTCATTAACATCGATATGAATGTGAGAAATGCTAGAATGACTTACATTGTGAA
TTCACAATGTAAGTCATTCTAGCATTTCTCACATTCATATCGATGTTAATGAATCTAGATAGATATATATGTCTAGATTCATTAACATTAATATGAATGT[G/T,A]
GGAAATGCTAGAATGACTTACATTGTGAAACGGAGGGAGTACCTATCAACCGTTTTGGAACCATTCTAGTTCTAGGATGACAAAGTGAAGACATTTCCCG
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 | 99.20% | 0.70% | 0.00% | 0.00% | T: 0.08% |
All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Aus | 269 | 91.10% | 7.40% | 0.00% | 0.00% | T: 1.49% |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
Intermediate | 90 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0724293530 | C -> A | LOC_Os07g40540.1 | downstream_gene_variant ; 2855.0bp to feature; MODIFIER | silent_mutation | Average:48.112; most accessible tissue: Callus, score: 81.73 | N | N | N | N |
vg0724293530 | C -> A | LOC_Os07g40550.1 | intron_variant ; MODIFIER | silent_mutation | Average:48.112; most accessible tissue: Callus, score: 81.73 | N | N | N | N |
vg0724293530 | C -> A | LOC_Os07g40550.2 | intron_variant ; MODIFIER | silent_mutation | Average:48.112; most accessible tissue: Callus, score: 81.73 | N | N | N | N |
vg0724293530 | C -> A | LOC_Os07g40550.3 | intron_variant ; MODIFIER | silent_mutation | Average:48.112; most accessible tissue: Callus, score: 81.73 | N | N | N | N |
vg0724293530 | C -> T | LOC_Os07g40540.1 | downstream_gene_variant ; 2855.0bp to feature; MODIFIER | silent_mutation | Average:48.112; most accessible tissue: Callus, score: 81.73 | N | N | N | N |
vg0724293530 | C -> T | LOC_Os07g40550.1 | intron_variant ; MODIFIER | silent_mutation | Average:48.112; most accessible tissue: Callus, score: 81.73 | N | N | N | N |
vg0724293530 | C -> T | LOC_Os07g40550.2 | intron_variant ; MODIFIER | silent_mutation | Average:48.112; most accessible tissue: Callus, score: 81.73 | N | N | N | N |
vg0724293530 | C -> T | LOC_Os07g40550.3 | intron_variant ; MODIFIER | silent_mutation | Average:48.112; most accessible tissue: Callus, score: 81.73 | N | N | N | N |
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