Hi,
we assembled one 150bp paired-end illumina sample with spades 3.10 and got about 400 contigs with a size of > 1kb.
Afterwards we scanned for SNPs with samtools/varscan with the same fastq-files in the assembly made out of these.
I know this doesn't make much sense :-), but samtools called some SNPs and we can see them in IGV, so they are really there.
How is this even possible, that we find a SNP with the same fastq files, of which the assembly is made of?
we assembled one 150bp paired-end illumina sample with spades 3.10 and got about 400 contigs with a size of > 1kb.
Afterwards we scanned for SNPs with samtools/varscan with the same fastq-files in the assembly made out of these.
I know this doesn't make much sense :-), but samtools called some SNPs and we can see them in IGV, so they are really there.
How is this even possible, that we find a SNP with the same fastq files, of which the assembly is made of?