Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,221,311	A→G	pseudogene (927/1436 nt)	mdtQ ←	multidrug resistance outer membrane protein MdtQ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,221,311	0	A	G	100.0%	58.6 / NA	18	pseudogene (927/1436 nt)	mdtQ	multidrug resistance outer membrane protein MdtQ
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (6/12);  total (6/12)

CCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAACAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGACTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTACCCCAGTTCATCAGGAAGCTGGCTTGCCACTTTCGGCAACGCGACCGGTTTAAGCTTCAATGACTTTGTCTGG  >  NZ_CP009273/2221175‑2221438                                                                                                                                         |                                                                                                                                ccTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAACAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCt                                                                                                                               <  1:440953/139‑1 (MQ=255)     ccGTAACGCCCATTTGCTGCGCGGAATGACGGAACAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCa                                                                                                                             <  2:117946/137‑1 (MQ=255)      cGTAACGCCCATTTGCTGCGCGGAATGACGGAACAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACg                                                                                                                          <  1:392027/139‑1 (MQ=255)                                     aaCAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCccgcc                                                                                           >  1:403724/1‑139 (MQ=255)                                       cAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCgg                                                                                         >  2:309460/1‑139 (MQ=255)                                           tCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCa                                                                                     <  1:303036/139‑1 (MQ=255)                                             gCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGt                                                                                   <  1:26249/139‑1 (MQ=255)                                                    tGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTg                                                                                                 <  1:397325/118‑1 (MQ=255)                                                    tGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTg                                                                                                 >  2:397325/1‑118 (MQ=255)                                                                            gCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCccgccg                                                                                          >  1:373689/1‑101 (MQ=255)                                                                            gCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCccgccg                                                                                          <  2:373689/101‑1 (MQ=255)                                                                            gCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTACCCCAGTTCATCAGGAAGCTGGc                                                    >  2:389541/1‑139 (MQ=255)                                                                               aTCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTACCCCAGTTCATCAGGAAGCTGGCTTg                                                 <  2:407399/139‑1 (MQ=255)                                                                                                    aaTGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTACCCCAGTTCATCAGGAAGCTGGCTTGCCACTTTCGGCAACGCGACCg                            >  2:315538/1‑139 (MQ=255)                                                                                                                 ccGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTACCCCAGTTCATCAGGAAGCTGGCTTGCCACTTTCGGCAACGCGACCGGTTTAAGCTTCa                <  1:217089/138‑1 (MQ=255)                                                                                                                      tCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTACCCCAGTTCATCAGGAAGCTGGCTTGCCACTTTCGGCAACGCGACCGGTTTAAGCTTCAATGACt          <  1:5046/139‑1 (MQ=255)                                                                                                                               cTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTACCCCAGTTCATCAGGAAGCTGGCTTGCCACTTTCGGCAACGCGACCGGTTTAAGCTTCAATGACTTTGTCTgg  <  1:397322/138‑1 (MQ=255)                                                                                                                               cTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTACCCCAGTTCATCAGGAAGCTGGCTTGCCACTTTCGGCAACGCGACCGGTTTAAGCTTCAATGACTTTGTCTgg  <  1:315538/138‑1 (MQ=255)                                                                                                                                         |                                                                                                                                CCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAACAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGACTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTACCCCAGTTCATCAGGAAGCTGGCTTGCCACTTTCGGCAACGCGACCGGTTTAAGCTTCAATGACTTTGTCTGG  >  NZ_CP009273/2221175‑2221438

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑