These SNPs were missing in the master genome annotation table and had only the contig line. Therefore these were not written out in the snp annotation file. I have manually added these lines at the end of the SNP annotation table in the lyc_dubois/annotation folder but I need to fix the script to account for these SNPs
V1 V2
764 1036
764 1063
764 1079
764 1084
1143 3161
1143 3187
1143 3193
1170 182
1170 204
1170 210
1170 229
1170 235
1170 257
1558 129
1558 132
1558 144
1558 160
1558 168
1558 174