[Genome] potential bug in DM3 phastcons -- addition

[Michael Hiller]

I found that this double-assignment occurs at multiple places in DM3.

chr2R.pp
    position 5000001

chr3L.pp
    position 7000001
    position 11000001
    position 19000001

chr3R.pp .....
    position 7000001
    position 20000001
    position 25000001

chrX.pp
    position 12000001
    position 14000001

Best,
Michael

Michael Hiller wrote:
> Dear Genome Browser team,
>
> I suspect that there is a minor bug in the Phastcons scores for DroMel 
> (assembly DM3).
> Using the table browser to get the values chr2R:4999997-5000009
> position 5000001 has two values, as shown below.
>
> Furthermore, looking at this region with the browser, position 5000003 
> has a lower score than the position up and downstream. However, in the 
> list below, 5000004 has the lowest value. So, somehow this double 
> count for position 5000001 affects the counting.
>
> What is the correct score for that position?
>
> Thanks and best regards,
> Michael
>
> track type=wiggle_0 name="Conservation" description="12 Flies, Mosquito, Honeybee, Beetle Multiz Alignments & phastCons Scores"
> #	output date: 2008-04-28 13:13:14 UTC
> #	chrom specified: chr2R
> #	position specified: 4999997-5000009
> #	This data has been compressed with a minor loss in resolution.
> #	(Worst case: 0.0078125)  The original source data
> #	(before querying and compression) is available at 
> #		http://hgdownload.cse.ucsc.edu/downloads.html
> variableStep chrom=chr2R span=1
> 4999997	0.984252
> 4999998	0.992126
> 4999999	0.992126
> 5000000	0.992126
> 5000001	0.992126
> 5000001	0.425197
> 5000002	0.566929
> 5000003	0.511811
> 5000004	0.338583
> 5000005	0.503937
> 5000006	0.559055
> 5000007	0.700787
> 5000008	0.905512
> 5000009	0.897638
>
>
> -- 
> Michael Hiller, Dr. rer. nat.
> Bioinformatics - Inst. of Computer Science
> University Freiburg
> Tel: +49 (0761) 203 8254
> http://www.bioinf.uni-freiburg.de/~hiller
>   



-- 
Michael Hiller, Dr. rer. nat.
Bioinformatics - Inst. of Computer Science
University Freiburg
Tel: +49 (0761) 203 8254
http://www.bioinf.uni-freiburg.de/~hiller