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%	84.0 / NA	25	pseudogene (927/1436 nt)	mdtQ	multidrug resistance outer membrane protein MdtQ
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (9/16);  total (9/16)

CCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAACAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGACTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTACCCCAGTTCATCAGGAAGCTGGCTTGCCACTTTCGGCAACGCGACCGGTTTAAGCTTCAATGA  >  NZ_CP009273/2221175‑2221428                                                                                                                                         |                                                                                                                      ccTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAACAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCt                                                                                                                     <  1:275608/139‑1 (MQ=255) ccTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAACAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCt                                                                                                                     <  1:490603/139‑1 (MQ=255)     ccGTAACGCCCATTTGCTGCGCGGAATGACGGAACAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCt                                                                                                                     >  2:580671/1‑135 (MQ=255)     ccGTAACGCCCATTTGCTGCGCGGAATGACGGAACAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCt                                                                                                                     <  1:580671/135‑1 (MQ=255)          aCGCCCATTTGCTGCGCGGAATGACGGAACAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTAc                                                                                                             >  2:222965/1‑138 (MQ=255)             cccATTTGCTGCGCGGAATGACGGAACAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGt                                                                                                         >  2:324310/1‑139 (MQ=255)                      tgcGCGGAATGACGGAACAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCt                                                                                                                     <  2:574474/118‑1 (MQ=255)                      tgcGCGGAATGACGGAACAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCt                                                                                                                     >  1:574474/1‑118 (MQ=255)                                    gAACAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCccgc                                                                                  <  1:222965/139‑1 (MQ=255)                                         gATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTCCCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGc                                                                             <  1:141243/139‑1 (MQ=255)                                          aTCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGc                                                                             >  1:15474/1‑138 (MQ=255)                                              cTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTa                                                                        <  1:161700/139‑1 (MQ=255)                                              cTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTa                                                                        <  2:520083/139‑1 (MQ=255)                                                   gTGCAACGCATCCTGTTGCAGGAAGTCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAg                                                                   <  2:71864/139‑1 (MQ=255)                                                         cGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTTAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTAccc                                                              >  1:112077/1‑138 (MQ=255)                                                         cGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTAcccc                                                             <  1:379519/139‑1 (MQ=255)                                                                            gCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTACCCCAGTTCATCAGGAAGCTGGc                                          >  2:112947/1‑139 (MQ=255)                                                                                              ggATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTACCCCAGTTCATCAGGAAGCTGGCTTGCCACTTTCGGCAAcg                        >  2:438686/1‑139 (MQ=255)                                                                                                 tAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTACCCCAGTTCATCAGGAAGCTGGCTTGCCACTTTCGGCAACGCGa                     <  1:324310/139‑1 (MQ=255)                                                                                                 tAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTACCCCAGTTCATCAGGAAGCTGGCTTGCCACTTTCGGCAACGCGa                     <  1:131584/139‑1 (MQ=255)                                                                                                   aaaTGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTACCCCAGTTCATCAGGAAGCTGGCTTGCCACTTTCGGCAACGCGAc                    <  1:460972/138‑1 (MQ=255)                                                                                                   aaaTGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTACCCCAGTTCATCAGGAAGCTGGCTTGCCACTTTCGGCAACGCGAc                    <  2:112077/138‑1 (MQ=255)                                                                                                                    cATCAATGGTGCTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTACCCCAGTTCATCAGGAAGCTGGCTTGCCACTTTCGGCAACGCGACCGGTTTAAGCTTCAATGa  <  1:112947/139‑1 (MQ=255)                                                                                                                               cTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTACCCCAGTTCATCAGGAAGCTGGCTTGCCACTTTCGGCAACGCGa                     <  2:250360/109‑1 (MQ=255)                                                                                                                               cTTAGCGATGGCTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTACCCCAGTTCATCAGGAAGCTGGCTTGCCACTTTCGGCAACGCGa                     >  1:250360/1‑109 (MQ=255)                                                                                                                                         |                                                                                                                      CCTGCCGTAACGCCCATTTGCTGCGCGGAATGACGGAACAGATCGCTTAAGTGCAACGCATCCTGTTGCAGGAAGGCCATCAGGTTGATGTCAGGATAAAATGCCGCTTTTGCCGCATCAATGGTGCTTAGCGATGACTCAACGTACCAGTGCGCCGCCTGCAAATCTGCCCGCCGGGCCAGTAAGGAGTACCCCAGTTCATCAGGAAGCTGGCTTGCCACTTTCGGCAACGCGACCGGTTTAAGCTTCAATGA  >  NZ_CP009273/2221175‑2221428

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑