1. To visualise the general taxonomic profile up to Phylum level:

SELECT final_domain, final_phylum, count(final_phylum) FROM taxonomy
WHERE final_phylum not null
GROUP BY final_phylum
ORDER BY final_domain ASC


2. To visualise transcript distribution: 

SELECT rna_type, count(rna_type) FROM taxonomy
GROUP BY rna_type
ORDER BY count(rna_type) DESC


3. To visualise non-redundant hits from the nucleotide homology search in the "mRNA" category:

SELECT nucl_hit, function_type, count(nucl_hit) FROM taxonomy
WHERE rna_type like "mrna"
GROUP BY nucl_hit
ORDER BY count (nucl_hit) DESC


4. To visualise non-redundant hits from the protein homology search in the "Revise" category:

SELECT prot_hit, function_type, COUNT(prot_hit) FROM taxonomy
WHERE rna_type like "Revise"
GROUP BY prot_hit
ORDER BY count (prot_hit) DESC


5. To visualise "mRNA" and "revise" rows with ip2go/eggnog assignment in descending order:

SELECT sequence, coverage, rna_type, function_type, final_domain, final_phylum, prot_hit, prot_Evalue, nucl_hit, nucl_Evalue FROM taxonomyfinal
WHERE (rna_type LIKE "mRNA" OR rna_type LIKE "revise") AND function_type NOTNULL
ORDER BY coverage DESC


6. To visualise "mRNA" and "revise" rows without ip2go/eggnog assignment in descending order:

SELECT sequence, coverage, rna_type, final_domain, final_phylum, prot_hit, prot_Evalue, nucl_hit, nucl_Evalue FROM taxonomyfinal
WHERE (rna_type LIKE "mRNA" OR rna_type LIKE "revise") AND function_type isnull
ORDER BY coverage DESC