The mutation shows up near the root of the tree

[Takkoona]

Describe the bug

The mutation shows up near the root of the tree when visualizing the result of fixationSites.

To Reproduce

The tree and sequence alignment file are uploaded. H1N1_HA.zip

Screenshots

Version info:

R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ggtree_2.2.1       treeio_1.12.0      RColorBrewer_1.1-2 ggrepel_0.8.2     
[5] ggplot2_3.3.2      aplot_0.0.4        sitePath_1.5.20    jsonlite_1.7.0    
[9] ape_5.4           

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6        BiocManager_1.30.10 pillar_1.4.4       
 [4] compiler_4.0.0      base64enc_0.1-3     tools_4.0.0        
 [7] digest_0.6.25       uuid_0.1-4          tidytree_0.3.3     
[10] evaluate_0.14       lifecycle_0.2.0     tibble_3.0.1       
[13] gtable_0.3.0        nlme_3.1-148        lattice_0.20-41    
[16] pkgconfig_2.0.3     rlang_0.4.6         IRdisplay_0.7.0    
[19] rvcheck_0.1.8       patchwork_1.0.1     IRkernel_1.1       
[22] parallel_4.0.0      gridExtra_2.3       withr_2.2.0        
[25] repr_1.1.0          dplyr_1.0.0         generics_0.0.2     
[28] vctrs_0.3.1         ade4_1.7-15         grid_4.0.0         
[31] tidyselect_1.1.0    glue_1.4.1          R6_2.4.1           
[34] pbdZMQ_0.3-3        seqinr_3.6-1        tidyr_1.1.0        
[37] purrr_0.3.4         magrittr_1.5        MASS_7.3-51.6      
[40] scales_1.1.1        htmltools_0.5.0     ellipsis_0.3.1     
[43] colorspace_1.4-1    lazyeval_0.2.2      munsell_0.5.0      
[46] crayon_1.3.4