How to get complete SNPs list using Mauve

Question

[Paul]

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.