Hello, I'm trying to call variants using samtools and bcftools and (for unknown reasons) I get incorrect base in the REF column of the resulting VCF file; example:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  ../algn/algn_400K.sorted.bam
...    226300  .       T       C       119     .       DP=465;VDB=0.0418;AF1=0.5;AC1=1;DP4=135,80,131,105;MQ=20;FQ=105;PV4=0.13,0.27,1,1       GT:PL:GQ    0/1:149,0,132:99

But when I check the above position in the reference, the actual base seems to be G:

In [18]: from Bio import SeqIO
In [19]: [ref] = SeqIO.parse(open("MG1655-K12.fasta"), "fasta")
In [20]: ref[226300] 
Out[20]: 'G'

Here's a summary of what I did to obtain the VCF:

$ samtools mpileup -uf MG1655-K12.fasta algn_400K.sorted.bam > 400K.raw.bcf
$ bcftools view -bvcg 400K.raw.bcf > 400K.vcf

Any hints on why this might happen?