Update README.md

README.md

@@ -32,7 +32,7 @@ File                                 PASS    LowQual  Percent_LowQual  Non-exclu
 **Plot_Low_Qual_SNV_Distribution.R** - example R plotting script - visualises the distribution of low qual SNV calls throughout the reference sequence both before an after the removal of those falling within repetitive and phage regions (normally excluded for phylogenetic analysis). 
 
 #### Example plot from above R code
-- Note that '--save_high_lowqual True' must be used with the above python script to save compatible vcf files (converted from bcf) for use with the R script. The default is 'False' as the files can be very large (~700Mb).  It may be worth changing the percentage cutoff (10% non-excluded lowqual SNVs) in the code for saving vcfs depending on the QC issue being diagnosed.
+- Note that '--save_high_lowqual True' must be used with the above python script to save compatible vcf files (converted from bcf) for use with the R script. The default is 'False' as the files can be very large (~700Mb).  It may be worth changing the percentage cutoff (10% non-excluded lowqual SNVs) in the code for saving vcfs depending on the QC issue being diagnosed.  Red points indicate the alternative allele, black points indicate the reference allele.
 - For other more sophisticatd vcf visualisation options please see: https://github.com/zadyson/SNV_plotter 
 ![image](https://user-images.githubusercontent.com/8507671/141644457-7f01fa9c-bc63-4ea9-b455-7f0cac2391a8.png)