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Detailed information for vg1205718847:

Variant ID: vg1205718847 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 5718847
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACGATCGGCGAGAAGTAAATAAACGTTCTTGAGATCCTGTTATTTTCAAAATTCCGATCACCTCGCCTCACGCGGAAGAGAAAAATCTTTGTAGGGCGGC[A/G]
CGGGCAAAGGCGGCTCAAGGCGGGACTGATGCCGCTTCCAGCGTGTCCCCTGCGGCGACCTCGACAGGAGTCGTGGTCGGTACTAAGGACTAGGAGGTGG

Reverse complement sequence

CCACCTCCTAGTCCTTAGTACCGACCACGACTCCTGTCGAGGTCGCCGCAGGGGACACGCTGGAAGCGGCATCAGTCCCGCCTTGAGCCGCCTTTGCCCG[T/C]
GCCGCCCTACAAAGATTTTTCTCTTCCGCGTGAGGCGAGGTGATCGGAATTTTGAAAATAACAGGATCTCAAGAACGTTTATTTACTTCTCGCCGATCGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.10% 37.90% 0.00% 0.00% NA
All Indica  2759 95.50% 4.50% 0.00% 0.00% NA
All Japonica  1512 6.30% 93.70% 0.00% 0.00% NA
Aus  269 62.80% 37.20% 0.00% 0.00% NA
Indica I  595 98.80% 1.20% 0.00% 0.00% NA
Indica II  465 96.10% 3.90% 0.00% 0.00% NA
Indica III  913 94.90% 5.10% 0.00% 0.00% NA
Indica Intermediate  786 93.30% 6.70% 0.00% 0.00% NA
Temperate Japonica  767 10.30% 89.70% 0.00% 0.00% NA
Tropical Japonica  504 2.60% 97.40% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 36.70% 63.30% 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
vg1205718847 A -> G LOC_Os12g10680.1 intron_variant ; MODIFIER silent_mutation Average:20.078; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N