kma output

[daoerxianqiao]

hi

about kma out put ,i notice it comes out ‘resfinder_kma’and other files.like pheno_table.txt、ResFinder_results.txt…but it didn’t give a

result . only ‘resfinder_kma’have result .my input file is fastq file .if use fastq to analyse only gives result in ‘resfinder_kma’?

and my parameter ‘-l 0.6 -t 0.8’ seems like doesn’t work.because the output file Template_Identity only 40.99.

and can you give me the four ‘Template_Identity、Template_Coverage、Query_Identity、Query_Coverage ’ detailed description.and the parameter ‘-l 0.6 -t 0.8’ influence which of them.

thank you for your time in these.

[daoerxianqiao]

and i find Query_Coverage over 1,how is the result comes out ?

[daoerxianqiao]

I really need to know the answer，someone can help me solve these questions?Thank you.

[Maja Weiss]

Hi,

Thank you for your patience, and I hope this will answer your questions.

The thresholds are hold against the KMA output to decide which will be counted as a hit by ResFinder. -l 0.6 will mean that the Template_coverage needs to be 60% or more. -t 0.8 will result in a hit in ResFinder if the Template_identity is 80% or above.

The KMA output is only an intermediate result so in your case, since the template identity is below 80% this will not result in a hit in ResFinder.

Template relates to the gene sequence from the database, Template_Coverage is how much of the template is covered by the query sequence, which is your input sequence. The Query_Coverage is then how much of the query sequence is covered by the template. Template_Identity is the number of matching nucleotides between the template and the query divided by the length of the template, while Query_Identity is number of matching nucleotides divided by the query length.

Best regards,

Maja

[daoerxianqiao]

thank you for your reply really!!