[Genome] a question about segmental duplication track

[Kayla Smith]

Hello Zhao Hao,

Querying our tables, I find there is only one row corresponding to the 
name of the segmental duplication you've listed:

mysql> select * from genomicSuperDups where name like "chr7:143070349";
+------+-------+------------+-----------+----------------+--------+--------+------------+------------+-----------+-----------+-----+-------------+------------+---------+-------+------+-----------------------------+--------+--------+--------+--------+--------+-----------+--------------+----------------+-----------+----------------+-----------+------------+
| bin  | chrom | chromStart | chromEnd  | name           | score  | 
strand | otherChrom | otherStart | otherEnd  | otherSize | uid | 
posBasesHit | testResult | verdict | chits | ccov | alignfile 
         | alignL | indelN | indelS | alignB | matchB | mismatchB | 
transitionsB | transversionsB | fracMatch | fracMatchIndel | jcK       | 
k2K        |
+------+-------+------------+-----------+----------------+--------+--------+------------+------------+-----------+-----------+-----+-------------+------------+---------+-------+------+-----------------------------+--------+--------+--------+--------+--------+-----------+--------------+----------------+-----------+----------------+-----------+------------+
| 1675 | chr7  |  142928984 | 142994356 | chr7:143070349 | 814215 | - 
    | chr7       |  143070349 | 143135726 | 158821424 |   0 | 
1000 | N/A        | N/A     | N/A   | N/A  | align_both//0022/both111382 
|  65337 |     27 |     77 |  27444 |  65193 |       144 |           99 
|             45 |  0.997796 |       0.997384 | 0.0022072 | 0.00220766 |
+------+-------+------------+-----------+----------------+--------+--------+------------+------------+-----------+-----------+-----+-------------+------------+---------+-------+------+-----------------------------+--------+--------+--------+--------+--------+-----------+--------------+----------------+-----------+----------------+-----------+------------+
1 row in set (0.01 sec)

One possibility of what's happening is that you might have "self-defined 
regions" of two different regions that both overlap this segmental 
duplication.   If this is the case, try creating a Custom Track instead 
of using the self-defined regions.  Instructions for Custom Tracks are here:

http://genome.ucsc.edu/goldenPath/help/customTrack.html

I hope this information is helpful to you.  Please don't hesitate to 
contact us again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group



ZHAO Hao wrote:
> Hi there,
> 
>  
> 
> May I ask something about the Segmental Duplication track?
> 
>  
> 
> I downloaded some SDs from this track in some self-defined regions. But
> I found that sometimes two SDs have the same information.
> 
> Here is an example:
> 
> 1675     chr7      142928984        142994356        chr7:143070349
> 814215  -           chr7      143070349        143135726
> 158821424        0          1000     N/A       N/A       N/A       N/A
> align_both//0022/both111382       65337   27         77            27444
> 65193   144       99         45         0.997796           0.997384
> 0.0022072         0.00220766
> 
> 1675     chr7      142928984        142994356        chr7:143070349
> 814215  -           chr7      143070349        143135726
> 158821424        0          1000     N/A       N/A       N/A       N/A
> align_both//0022/both111382       65337   27         77            27444
> 65193   144       99         45         0.997796           0.997384
> 0.0022072         0.00220766
> 
>  
> 
> The values of each item of the two SDs are the same. Could you explain
> that?
> 
>  
> 
> Thanks
> 
>  
> 
> Zhao Hao
> 
> Genome Institute of Singapore
> 
>  
> 
>  
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome