Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,885,585	T→C	F204S (TTC→TCC)	mdtL →	multidrug efflux MFS transporter MdtL

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,885,585	0	T	C	100.0%	186.4 / NA	53	F204S (TTC→TCC)	mdtL	multidrug efflux MFS transporter MdtL
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (29/24);  total (29/24)

TTCTGGGCGATGGCAATGATGGGCATCGCGGTACTGATGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTTCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAACACGTCACCGGTATTGCTGATGGAAATCATGGGGTTTGAGCGCGGTGAATACGCCACCATTATGGCGCTGACCGCTGG  >  NZ_CP009273/3885452‑3885720                                                                                                                                      |                                                                                                                                        ttCTGGGCGATGGCAATGATGGGCATCGCGGTACTGATGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCt                                                                                                                                      >  2:128936/1‑137 (MQ=255) ttCTGGGCGATGGCAATGATGGGCATCGCGGTACTGATGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCt                                                                                                                                      <  2:498002/137‑1 (MQ=255)      ggCGATGGCAATGATGGGCATCGCGGTACTGATGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCgt                                                                                                                               >  1:217867/1‑139 (MQ=255)      ggCGATGGCAATGATGGGCATCGCGGTACTGATGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCgt                                                                                                                               >  2:384580/1‑139 (MQ=255)      ggCGATGGCAATGATGGGCATCGCGGTACTGATGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCgt                                                                                                                               >  1:805127/1‑139 (MQ=255)      ggCGATGGCAATGATGGGCATCGCGGTACTGATGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCgt                                                                                                                               >  2:541717/1‑139 (MQ=255)       gCGATGGCAATGATGGGCATCGCGGTACTGATGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCgtg                                                                                                                              <  1:384580/139‑1 (MQ=255)           tGGCAATGATGGGCATCGCGGTACTGATGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGtgttgt                                                                                                                          <  2:795126/139‑1 (MQ=255)           tGGCAATGATGGGCATCGCGGTACTGATGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGtgttgt                                                                                                                          >  1:725782/1‑139 (MQ=255)                atgatgGGCATCGCGGTACTGCTGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATca                                                                                                                     >  2:756589/1‑139 (MQ=255)                 tgatgGGCATCGCGGTACTGATGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATcac                                                                                                                    <  2:171931/139‑1 (MQ=255)                       gCATCGCGGTACTGATGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCt                                                                                                              <  1:460413/139‑1 (MQ=255)                        cATCGCGGTACTGATGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCt                                                                                                              >  2:841799/1‑138 (MQ=255)                        cATCGCGGTACTGATGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCt                                                                                                              >  2:517779/1‑138 (MQ=255)                                     aTGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCgtg                                                                                                                              <  1:708455/109‑1 (MQ=255)                                     aTGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCgtg                                                                                                                              >  2:708455/1‑109 (MQ=255)                                     aTGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGtgttgt                                                                                                                          <  1:413450/113‑1 (MQ=255)                                     aTGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGtgttgt                                                                                                                          >  2:413450/1‑113 (MQ=255)                                     aTGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGa                                                                                                >  1:169441/1‑139 (MQ=255)                                       gttgtCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATc                                                                                              >  2:68237/1‑139 (MQ=255)                                          gtCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATcac                                                                                                                    >  2:66874/1‑114 (MQ=255)                                          gtCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATcac                                                                                                                    <  1:66874/114‑1 (MQ=255)                                          gtCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCt                                                                                            >  1:452377/1‑138 (MQ=255)                                          gtCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCt                                                                                            >  2:299620/1‑138 (MQ=255)                                          gtCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCt                                                                                            >  1:842624/1‑138 (MQ=255)                                          gtCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCt                                                                                            >  1:571701/1‑138 (MQ=255)                                          gtCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCt                                                                                            >  2:599519/1‑138 (MQ=255)                                                     ttttAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCt                                                                                                              <  1:317792/109‑1 (MQ=255)                                                     ttttAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCt                                                                                                              >  2:317792/1‑109 (MQ=255)                                                     ttttAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCaa                                                                                <  1:517779/139‑1 (MQ=255)                                                         aaaaGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAacac                                                                             <  2:848747/138‑1 (MQ=255)                                                         aaaaGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAacac                                                                             <  2:169441/138‑1 (MQ=255)                                                                             cccccGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAACACGTCACCGGTATTGCTGATGGa                                                        <  2:802349/139‑1 (MQ=255)                                                                              ccccGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCt                                                                                                              <  1:273907/84‑1 (MQ=255)                                                                              ccccGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCt                                                                                                              >  2:273907/1‑84 (MQ=255)                                                                                  gCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAACACGTCACCGGTATTGCTGATGGAAATCa                                                   <  2:842624/139‑1 (MQ=255)                                                                                       ttCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAACACGTCACCGGTATTGCTGATGGAAATCATgggg                                              >  2:463362/1‑139 (MQ=255)                                                                                           gATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAACACGTCACCGGTATTGCTGATGGAAATCATGGGGttt                                           >  1:542371/1‑138 (MQ=255)                                                                                            gataaCCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAACACGTCACCGGTATTGCTGATGGAAATCATGGGGttt                                           >  1:828923/4‑137 (MQ=255)                                                                                                aCCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAACACGTCACCGGTATTGCTGATGGAAATCATGGGGTTTGAgcgc                                     >  1:381083/1‑139 (MQ=255)                                                                                                 ccACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAACACGTCACCGGTATTGCTGATGGAAATCATGGGGTTTGAGcgcg                                    <  1:232739/139‑1 (MQ=255)                                                                                                 ccACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAACACGTCACCGGTATTGCTGATGGAAATCATGGGGTTTGAGcgcg                                    <  1:463362/139‑1 (MQ=255)                                                                                                      agaAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAACACGTCACCGGTATTGCTGATGGAAATCATGGGGTTTGAGCGCGGTGaa                               <  2:452377/139‑1 (MQ=255)                                                                                                      agaAAATAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAACACGTCACCGGTATTGCTGATGGAAATCATGGGGTTTGAGCGCGGTGaa                               <  2:538272/139‑1 (MQ=255)                                                                                                           aTAGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAACACGTCACCGGTATTGCTGATGGAAATCATGGGGTTTGAGCGCGGTGAATACGc                          <  1:703998/139‑1 (MQ=255)                                                                                                             aGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCaa                                                                                <  1:778472/83‑1 (MQ=255)                                                                                                             aGCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCaa                                                                                >  2:778472/1‑83 (MQ=255)                                                                                                              gCGAGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAACACGTCACCGGTATTGCTGATGGAAATCATGGGGTTTGAGCGCGGTGAATACGccac                       <  1:299620/139‑1 (MQ=255)                                                                                                                 aGTCGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAACACGTCACCGGTATTGCTGATGGAAATCATGGGGTTTGAGCGCGGTGAATACGCCACCAt                    >  1:847635/1‑139 (MQ=255)                                                                                                                    cGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATcac                                                                                                                    <  1:319896/40‑1 (MQ=255)                                                                                                                    cGCTGCTTAACCGTTTTTCCCTCAGCCGTGTTGTTATcac                                                                                                                    >  2:319896/1‑40 (MQ=255)                                                                                                                        gctTAACCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAACACGTCACCGGTATTGCTGATGGAAATCATGGGGTTTGAGCGCGGTGAATACGCCACCATTATGgcg             >  1:356408/1‑139 (MQ=255)                                                                                                                            aaCCGTTTTTCCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAACACGTCACCGGTATTGCTGATGGAAATCATGGGGTTTGAGCGCGGTGAATACGCCACCATTATGGCGCt           <  2:725782/137‑1 (MQ=255)                                                                                                                                 ttttttCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAACACGTCACCGGTATTGCTGATGGAAATCATGGGGTTTGAGCGCGGTGAATACGCCACCATTATGGCGCTGACCGCt    >  2:133017/1‑139 (MQ=255)                                                                                                                                 tttttcCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAACACGTCACCGGTATTGCTGATGGAAATCATGGGGTTTGAGCGCGGTGAATACGCCACCATTATGGCGCTGACCGCt    >  2:462014/1‑139 (MQ=255)                                                                                                                                   tttcCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAACACGTCACCGGTATTGCTGATGGAAATCATGGGGTTTGAGCGCGGTGAATACGCCACCATTATGGCGCTGACCGCTgg  >  1:347741/1‑139 (MQ=255)                                                                                                                                      |                                                                                                                                        TTCTGGGCGATGGCAATGATGGGCATCGCGGTACTGATGTTGTCTTTGTTTATTTTAAAAGAAACGCGCCCAGCGGCCCCCGCAGCTTCGGATAAACCACGAGAAAATAGCGAGTCGCTGCTTAACCGTTTTTTCCTCAGCCGTGTTGTTATCACCACCCTCAGCGTTTCGGTGATCCTCACTTTCGTCAACACGTCACCGGTATTGCTGATGGAAATCATGGGGTTTGAGCGCGGTGAATACGCCACCATTATGGCGCTGACCGCTGG  >  NZ_CP009273/3885452‑3885720

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑