SNP detection by samtools returns dots under the reference columns

[Mithril]

Hello,
I have a very peculiar problem. I used samtools to get SNPs using the mpileup command. The commands that i used are as follows:

samtools mpileup -uf cpp34_contigs_nr_prinseq_good_NAF4.fasta aln-sorted.bam | bcftools view -bvcg - > var.raw.bc

bcftools view var.raw.bcf > var.flt.vcf

The .vcf file that i got had the follwing results:
#CHROM POS ID REF ALT QUAL
PT_34_209 159 . T C 7.8
PT_34_209 164 . C T 7.8
PT_34_209 655 . A G 7.8
PT_34_209 658 . G C 7.8
PT_34_209 659 . C G 7.8
PT_34_238 533 . T C 7.8
PT_34_238 600 . T C 7.8
PT_34_238 786 . A T 7.8
PT_34_238 789 . A C 7.8
PT_34_238 790 . T C 7.8
PT_34_238 791 . T G 7.8
PT_34_238 792 . T C 7.8
PT_34_238 793 . G T 7.8
PT_34_238 795 . T G 7.8
PT_34_258 561 . A G 7.8
PT_34_549 520 . T C 7.8

Could anybody please help me with this? and let me know how i can correct the problem between the reference column and the quality column?

[Alex Renwick]

I don't see any problem here. For example, the first row of you results says chromosome PT_34_209 has reference allele T at position 159 and a C snp was observed with quality 7.8, and there is no snp id for that position. What are you expecting to see that is not here?

[Mithril]

Ow... My bad. i just realised my mistake. thank you

[Alex Renwick]

Again I'll say that there is no problem. In the vcf format the entries are separated by tabs. A long entry (the chromosome, in this case) can make the columns look misaligned, but the downstream analysis tools will have no trouble parsing the file.