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Old 06-28-2010, 10:38 AM   #1
Bio.X2Y
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Location: Europe

Join Date: Apr 2010
Posts: 46
Default SAM Format - SEQ field '='

Hi,

I was just looking through the SAM format spec again and I've come across something that confuses me.

The text for the 'SEQ' field is:
"query SEQuence; = for a match to the reference; n/N/. for ambiguity; cases are not maintained"

In practice, I've never seen a "=" in the SEQ field; is this supposed to be an optional way of using the format, i.e. using a combination of "=" and "N" instead of the actual query sequence?

Thanks,
Bio
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