I am having multiple contigs for 1000s of genome, and each genome was mapped with the reference genome. I am using command line Mauve to extract all the SNPs from the alignments of contigs with the Reference genome. the command line used was
java org.gel.mauve.analysis.SnpExporter -f aln.xmfa -o aln.snps
And the list of SNPs I get for each genome is like the following:
SNP Ref GenWidePos1 sequence2Contig sequence2PosInContg sequence2GenWidePos2 GT Ref 55649 Contig_18 130 3255611 CT Ref 55553 Contig_76 226 3255707 AG Ref 54394 Contig_72 1394 3256875 AG Ref 51949 Contig_35 3839 3259320 TC Ref 50557 Cont
But there more SNPs present between the contigs and the reference, but mauve gives me only half of the SNPs and it stops in the middle. Like the last line in the above mentioned example.