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Detailed information for vg0226609424:

Variant ID: vg0226609424 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 26609424
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


AGGCCGGCCGGGTCGAGGGCGCCACCATTGGTCAATTGCCCTACACAAACCAAGCCGTCGGTAGGTCAGAAATGAAACATACTACTGTACATATCAAACC[G/A]
GAAAATGCGTTGAGCTCACCATAGGCAATGGCGGATCCGACGCCAGCGAAGACGAAGAGGAGGGTGGCGATGAACTCCGCCACGTAGGCCTTCACGGACG

Reverse complement sequence

CGTCCGTGAAGGCCTACGTGGCGGAGTTCATCGCCACCCTCCTCTTCGTCTTCGCTGGCGTCGGATCCGCCATTGCCTATGGTGAGCTCAACGCATTTTC[C/T]
GGTTTGATATGTACAGTAGTATGTTTCATTTCTGACCTACCGACGGCTTGGTTTGTGTAGGGCAATTGACCAATGGTGGCGCCCTCGACCCGGCCGGCCT

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 99.90% 0.10% 0.00% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0226609424 G -> A LOC_Os02g44080.1 intron_variant ; MODIFIER N Average:70.745; most accessible tissue: Zhenshan97 root, score: 86.891 N N N N