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NMmum2gxc. Nevertheless, the outputed table give you a first overview of the nature of the raw
alignment between the sequences of the two strains. Here, and in the subsequent files the prefix cis
is used to describe a chromosome-to-chromosome relationship while the prefix trans is used to flag
putative translocation events.
$ cat S3/BY_RM_gxcomp.out ## # Table of relationships to explore ## type ref qry T(match|ref) %(match|qry) %(match|ref) %(+|ref) %(-|ref) cis chrVIII supercontig_1.12 506622 0.938 0.900 1.000 0.000 trans chrVIII supercontig_1.17 15760 0.029 0.028 0.000 1.000 cis chrX supercontig_1.8 684930 0.976 0.918 1.000 0.000 cis chrVII supercontig_1.2 1032008 0.993 0.946 0.000 1.000 cis chrIX supercontig_1.14 400804 1.000 0.911 0.000 1.000 cis chrII supercontig_1.6 785026 1.000 0.965 0.000 1.000 cis chrXIV supercontig_1.7 763497 1.000 0.973 0.043 0.957 cis chrIII supercontig_1.15 300505 0.965 0.949 0.971 0.029 cis chrXV supercontig_1.3 1034494 0.975 0.948 1.000 0.000 cis chrVI supercontig_1.16 231275 0.938 0.856 1.000 0.000 trans chrVI supercontig_1.8 13642 0.055 0.050 1.000 0.000 cis chrXII supercontig_1.10 566426 0.554 0.525 1.000 0.000 cis chrXII supercontig_1.13 441487 0.432 0.409 1.000 0.000 cis chrXVI supercontig_1.4 882793 0.964 0.931 1.000 0.000 cis chrI supercontig_1.17 165518 0.992 0.719 0.000 1.000 cis chrXI supercontig_1.9 641056 1.000 0.962 1.000 0.000 cis chrV supercontig_1.11 545509 0.998 0.946 1.000 0.000 cis chrIV supercontig_1.1 1471886 0.995 0.961 0.000 1.000 cis chrXIII supercontig_1.5 884250 0.987 0.957 1.000 0.000 ## # Exploring cis relationships: wait... ## ## # Exploring trans relationships:wait... ## ## # Merge+Output results:wait... ##