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Posted: Thu Mar 01, 2012 7:56 pm
A student called reads in project 1774P12 that suggest a polymorphism. All three reads the student got had about 28 high quality bases in a region that only has reads from "danafos". What are the danafos reads and is this a polymorphism?
Posted: Thu Mar 01, 2012 7:58 pm
I should've said that the only high-quality reads are from danafos. The reads from the student had a different sequence than the danafos. The other reads are low quality or fake.
Posted: Thu Mar 01, 2012 8:53 pm
> What are the danafos reads and is this a polymorphism?
The danafos reads are derived from the fosmid library. The original whole genome shotgun assembly consists of reads from three different libraries: BAC's, fosmids, and subclones. Reads from subclones are named according to its plate and well position (e.g. 07552275G01.b1). The fosmid reads have the prefix danafos, followed by a unique ID. The "danafos" prefix allow Consed to recognize that these reads are derived from a different library with a larger insert size (i.e. 40kb) compared to the subclones (i.e. 3-5kb).
Based on the screenshot of the aligned reads window, there is insufficient evidence to conclude that the difference is caused by a polymorphism. An alternative hypothesis is that this region could have been misassembled. Either the reads generated by the custom oligos 5, 6, and 15 are at the wrong location or there is an error in the assembly piece and the danafos4471.g1 read. Because we expect the custom reads to be placed downstream of the primers from which the reads were derived, we can use the positions of the oligo tags to determine if the custom oligo reads have been misplaced.