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samtools pileup

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  • samtools pileup

    hi all :
    I am using BWA with default parameters, and i get my alignement file (.sam).
    Now with samtools, i am trying to call SNPs with pileup command :

    and i got :

    .
    chrY 186 T T 75 0 36 20 G,,.....,,,.,,..,-1g,., !eb^]$`%^d\aae^Y%UIB
    .
    .
    chrY 300 A A 42 0 37 6 .+2TC,..., !cb`_S

    i noticed that many lines contain the same base in the reference and the read sequence.
    is that's normal ? if yes what is that means , and if not, what is probably the explanation or the solution.
    thanks
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