Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,581,070	G→A	A39A (GCG→GCA)	acrD →	multidrug efflux RND transporter permease AcrD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,581,070	0	G	A	100.0%	178.5 / NA	45	A39A (GCG→GCA)	acrD	multidrug efflux RND transporter permease AcrD
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (17/28);  total (17/28)

ACGAGGTCCTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCGCCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGTGG  >  NZ_CP009273/2580938‑2581204                                                                                                                                     |                                                                                                                                       acGAGGTCCTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCg                                                                                                                                  <  1:781847/139‑1 (MQ=255)            ttttAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGa                                                                                                                         <  1:284304/137‑1 (MQ=255)              ttAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAg                                                                                                                        <  2:123823/136‑1 (MQ=255)              ttAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGt                                                                                                                       <  1:198743/137‑1 (MQ=255)              ttAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGt                                                                                                                       <  2:686461/137‑1 (MQ=255)                 aTGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCg                                                                                                                  >  2:563136/1‑139 (MQ=255)                 aTGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCg                                                                                                                  <  2:181515/139‑1 (MQ=255)                    gCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCt                                                                                                                <  2:483386/138‑1 (MQ=255)                     cGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTTGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTaa                                                                                                              <  2:667860/139‑1 (MQ=255)                      gAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAAc                                                                                                             >  1:827445/1‑139 (MQ=255)                               tATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCgg                                                                                                     <  1:377646/138‑1 (MQ=255)                                    aTCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCAt                                                                                                <  2:299723/138‑1 (MQ=255)                                    aTCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATc                                                                                               >  2:333608/1‑139 (MQ=255)                                               tttGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACg                                                                                     <  1:333608/138‑1 (MQ=255)                                                   ccTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTgg                                                                                 >  2:481714/1‑138 (MQ=255)                                                   ccTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGa                                                                                <  1:668048/139‑1 (MQ=255)                                                       ggTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGaaaa                                                                             >  1:567284/1‑138 (MQ=255)                                                           cTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCg                                                                        <  1:481714/139‑1 (MQ=255)                                                            tGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGt                                                                       >  2:409798/1‑139 (MQ=255)                                                               cAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGAc                                                                    <  1:18802/139‑1 (MQ=255)                                                                   ccTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAg                                                                >  1:65461/1‑139 (MQ=255)                                                                          tgtCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATc                                                          <  1:287040/138‑1 (MQ=255)                                                                            tCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCAt                                                                                                <  2:659595/98‑1 (MQ=255)                                                                            tCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCAt                                                                                                >  1:659595/1‑98 (MQ=255)                                                                            tCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACAcc                                                                         <  2:653702/121‑1 (MQ=255)                                                                            tCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACAcc                                                                         >  1:653702/1‑121 (MQ=255)                                                                            tCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAg                                                       <  1:2836/139‑1 (MQ=255)                                                                              tGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCg                                                                                                                  >  1:327776/1‑78 (MQ=255)                                                                              tGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCg                                                                                                                  <  2:327776/78‑1 (MQ=255)                                                                              tGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGc                                                      >  2:808319/1‑138 (MQ=255)                                                                                          tGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCgg                                         >  1:267366/1‑139 (MQ=255)                                                                                                 tttttCATTGCCAGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGa                                   >  1:447033/1‑138 (MQ=255)                                                                                                   tttCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATa                                 <  1:206592/138‑1 (MQ=255)                                                                                                   tttCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATa                                 <  2:2477/138‑1 (MQ=255)                                                                                                     tCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAAt                               <  1:650291/138‑1 (MQ=255)                                                                                                     tCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAAt                               <  2:567284/138‑1 (MQ=255)                                                                                                                  aaCAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGt                  <  1:421843/138‑1 (MQ=255)                                                                                                                         ccccGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCATCTCag          <  2:382452/139‑1 (MQ=255)                                                                                                                            cGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAAtctc                            >  1:734785/1‑118 (MQ=255)                                                                                                                            cGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAAtctc                            <  2:734785/118‑1 (MQ=255)                                                                                                                              aTCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAAtctc                            <  2:779630/116‑1 (MQ=255)                                                                                                                              aTCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAAtctc                            >  1:779630/1‑116 (MQ=255)                                                                                                                                 tcGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGc                                        <  1:683417/101‑1 (MQ=255)                                                                                                                                 tcGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGc                                        >  2:683417/1‑101 (MQ=255)                                                                                                                                 tcGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGTgg  >  2:330401/1‑139 (MQ=255)                                                                                                                                     |                                                                                                                                       ACGAGGTCCTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCGCCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGTGG  >  NZ_CP009273/2580938‑2581204

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑