Phred scores and Multiple/ Consensus reads

James VanEe jiv2 at cornell.edu
Fri Mar 15 15:58:49 EST 2002

Hi Laurence,
   I believe that Consed maintains confidence values for consensus
sequences and they are based on the depth of reads and the quality
scores of each component read at that base.  This doesn't answer your
question directly but I'm pretty sure that Consed has documentation
describing how these scores are derived. Your math looks good to me
but I haven't given it a lot of thought.

>Dear colleague,
>I have a question regarding Phred. If you have a base from a sequencing
>read that has a designated Phred score of 20 and the equivalent base
>from the complementary strand also has a designated score of 20, what
>would be the confidence value  in a concensus built from these two
>strands ??
>Given that each base has at Phred 20, by definition, a 1% chance of
>being wrong is the error rate for the resulting concensus 1% of 1%, in
>other words 1 in 10,000 that is q40 ?? If not how is the resulting Phred
>score computed ??
>Thanks for any assistance
>Laurence Hall
>Laurence S Hall
>Senior Research Associate
>Rubicon Genomics
>Suite G
>4370 Varsity Drive
>Ann Arbor
>MI 48108
>Tel. : (00) 1 734 677 2793
>Cell : (00) 1 734 727 5140
>Fax : (00) 1 734 477 9902/3
>EMail : hall at rubicongenomics.com
>            lhall48108 at yahoo.com

   James VanEe, Manager
   BRC Computing Facility
   171 Biotech Bldg, CU, Ithaca NY 14853
   (607) 254-4862 (fax4847)


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