[Genome] sequences mapped to the cow genome

[João Fadista]

Hello,
 
I have whole genome shotgun (WGS) sequences from the cow that were mapped to the cow genome using the SSAHA algorithm. So now I have a file where some regions in the genome have 1 or more WGS sequences addressed to it, with the respective score. 
 
Taking into account that the genome was from the Hereford breed and my WGS sequences are from other breed, I would like to know if it is possible to assess (with statistical significance) the structural variation between these 2 breeds.
I already plotted the number of WGS sequences as a function of the respective regions hitted in the genome and then I played with various score thresholds. With this I could see some parts of the genome being more hitted by my WGS sequences than others which could be a evidence of structural variation (if it is a region without repeats). 
 
I would also like to know if, using your genome and table browsers, it´s possible to have a nice graphical and text summary/description of my data like a structural variation profile.
 
 
Trimmed version of the file:

Score         Q_Name                           S_Name        Q_Start          Q_End          S_Start           S_End             Direction            #Bases                    identity          #Q_Bases            Freq

99             D34F6UT01DC4KM         Chr6               16                   124               35738256          35738364        Forward              109                           100.00                   124                     1

99             D34F6UT01EYJDA          Chr6                16                   124               35738256          35738364        Forward              109                           100.00                  124                      1

Note: ´Q´ stands for query sequence and ´S´ for sequence in the genome.
 
 
 

Best Regards,

João Fadista
Ph.d. student

 	
 	 AARHUS UNIVERSITET / UNIVERSITY OF AARHUS	
Faculty of Agricultural Sciences	
Dept. of Genetics and Biotechnology	
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E-mail:	 Joao.Fadista at agrsci.dk <mailto:Joao.Fadista at agrsci.dk> 	
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