Interpreting co-ordinates file

Question

[AP]

Hello everyone,

I got the coordinate file after aligning my query genome file to the reference genome file using MUMmer. Now I want to distinguish core and accessory genome using that coordinate file. But I do not know how I can do that. The coordinate file looks like this:

[S1]     [E1]  |     [S2]     [E2]  |  [LEN 1]  [LEN 2]  |  [% IDY]  |  [LEN R]  [LEN Q]  |  [COV R]  [COV Q]  | [TAGS]
===============================================================================================================================
     160      680  |  4898616  4898097  |      521      520  |    82.77  |  5906624  6559178  |     0.01     0.01  | CM010335.1 scaffold_1
     171      514  |    82222    81879  |      344      344  |    84.39  |  5906624   141341  |     0.01     0.24  | CM010335.1 scaffold_39
     216      705  |   852158   852649  |      490      492  |    86.87  |  5906624   890612  |     0.01     0.06  | CM010335.1 scaffold_12
     216      678  |    22395    22859  |      463      465  |    87.34  |  5906624   465278  |     0.01     0.10  | CM010335.1 scaffold_16
     216     1029  |    25724    24920  |      814      805  |    83.84  |  5906624   141858  |     0.01     0.57  | CM010335.1 scaffold_38
     216      565  |    53713    53367  |      350      347  |    85.14  |  5906624    70037  |     0.01     0.50  | CM010335.1 scaffold_75
     217      705  |  2323008  2322518  |      489      491  |    85.83  |  5906624  4306444  |     0.01     0.01  | CM010335.1 scaffold_5

I will appreciate your help.

Thanks,

Ambika

Answer 1

[Mensur Dlakic]

I don't think it matters much because you have so little sequence matching. Your longest match is less than 1000 bp, and query coverage is well below 1%. Either something went wrong during the comparison, or your queries are not related to the reference sequence.