Need help interpreting CoGe SynMap result
Entering edit mode
3 months ago
Lucas Peres ▴ 80

Hi, I'm a computer science student and I'm having some trouble understanding one of SynMap's outputs. This is the first time I'm using this tool, so my doubts may be very basic. The output I'm interested in is DAGChainer output in genomic coordinates. I pasted bellow a small sample of the file:

#1  5438.0  a61341_CP009354.1   b61370_CP018835.1   f   114  Mean Ks:  26.8037  Mean Kn: 0.1808
#Ks Kn  a<db_genome_id>_<chr>   chr1||start1||stop1||name1||strand1||type1||db_feature_id1||genome_order1||percent_id1  start1  stop1   b<db_genome_id>_<chr>   chr2||start2||stop2||name2||strand2||type2||db_feature_id2||genome_order2||percent_id2  start2  stop2   eval    block_score GEVO_link
3.3861  0.1466  a61341_CP009354.1   CP009354.1||2533113||2533958||cds-AIW14852.1||-1||CDS||3462596172||2299||71.04  2533958 2533113 b61370_CP018835.1   CP018835.1||999503||1000348||cds-ASA55073.1||-1||CDS||3463773201||923||71.04    1000348 999503  1.200000e-161   50
8.9127  0.0410  a61341_CP009354.1   CP009354.1||2534066||2534647||cds-AIW14853.1||-1||CDS||3462596173||2300||77.41  2534647 2534066 b61370_CP018835.1   CP018835.1||1000376||1000951||cds-ASA55074.1||-1||CDS||3463773202||924||77.41   1000951 1000376 5.000000e-143   100

Furthermore, there are other headers as follows (I omitted the actual data):

#1  2729.0  a61341_CP009354.1   b61370_CP018835.1   r   60  Mean Ks:  29.3942   Mean Kn: 0.1974
#1  367.0   a61341_CP009354.1   b61370_CP018836.1   f   8  Mean Ks:  42.0974    Mean Kn: 0.2392
#1  450.0   a61341_CP009355.1   b61370_CP018835.1   f   9  Mean Ks:  26.1880    Mean Kn: 0.1268
#1  391.0   a61341_CP009355.1   b61370_CP018835.1   r   9  Mean Ks:  38.5121    Mean Kn: 0.2237
#1  558.0   a61341_CP009355.1   b61370_CP018836.1   f   12  Mean Ks:  31.9494   Mean Kn: 0.2921
#1  464.0   a61341_CP009355.1   b61370_CP018836.1   r   10  Mean Ks:  58.8696   Mean Kn: 0.3136

I put the repeated headers, there are others (#2, #3, etc). Although I've already read the documentation regarding this particular output, still I don't understand what it means. As far as I know, each header starting with # indicates a synteny between the two chromosomes. The docs say that these can be repeated, and I don't understand what these repeats mean. Probably I'm missing something because I may lack some biological knowledge. Furthermore, could you explain what each row mean? The file itself already has a description for the columns, but I didn't quite get what each row mean.

Sorry if the question is too basic. As I don't have a background in biology, I'm in need of some assistance to interpret the output. Thanks for any help!

bioinformatics tool genomics genome • 154 views

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