Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,455,069	G→T	A7A (GCG→GCT)	unknown →	IncQ plasmid conjugative transfer protein TraQ (RP4 TrbM homolog)

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,455,069	0	G	T	100.0%	122.6 / NA	37	A7A (GCG→GCT)	unknown	IncQ plasmid conjugative transfer protein TraQ (RP4 TrbM homolog)
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (21/16);  total (21/16)

TTTCTACTTTGCGCATCATGCAGATAGTATTGAAATCTACGGTCAGCCGGCGCGTACCGAAGCCTATAAATACTGGTTACAGGCAAATGGGGTAAGTGCCAATATCAGTACATATCAGAAAGACCTATTAAAAAATAATGTCAATATAACTTTCAGGAAAGGAGTTAAAAATGAAAAAGCCCTTTAAAATTGGTGTAATCTTTCTTGCTTTATGCAGTATGAGCCAAATAAGCCATGCGGTGGATGAATTAACCGGTGATACCAAAACCGCCTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCATCCGCCGTTAAATAAGTTCTATTCAATTCGGGCTAAAAAACCACACGAAACATTAAAGAAACGTCGTAACTTTTTAAAACTATGCCCGGATGCTAGTG  >  1/1454831‑1455259                                                                                                                                                                                                                                               |                                                                                                                                                                                               tttCTACTTTGCGCATCATGCAGATAGTATTGAAATCTACGGTCAGCCGGCGCGTACCGAAGCCTATAAATACTGGTTACAGGCAAATGGGGTAAGCGCCAACATCAGCACACACCCAAAAGACTTGTTAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTa                                                                                                                                                                                    >  1:132505/1‑251 (MQ=255)      aCTTTGCGCATCATGCAGATAGTATTGAAATCTACGGTCAGCCGGCGCGTACCGAAGCCTATAAATACTGGTTACAGGCAAATGGGGTAAGCGCCAACATCAGCACACACCCAAAAGACTTGTTAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCgg                                                                                                                                                                               >  1:850524/1‑251 (MQ=255)           gcgcATCATGCAGATAGTATTGAAATCTACGGTCAGCCGGCGCGTACCGAAGCCTATAAATACTGGTTACAGGCAAATGGGGTAAGCGCCAACATCAGCACACACCCAAAAGACTTGTTAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATa                                                                                                                                                                          >  1:179385/1‑251 (MQ=255)                       gATAGTATTGAAATCTACGGTCAGCCGGCGCGTACCGAAGCCTATAAATACTGGTTACAGGCAAATGGGGTAAGCGCCAACATCAGCACACACCCAAAAGACTTGTTAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGctt                                                                                                                                                              >  1:416471/1‑249 (MQ=255)                           gTATTGAAATCTACGGTCAGCCGGCGCGTACCGAAGCCTATAAATACTGGTTACAGGCAAATGGGGTAAGCGCCAACATCAGCACACACCCAAAAGACTTGTTAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGa                                                                                                                                                          >  1:210422/1‑251 (MQ=255)                           gTATTGAAATCTACGGTCAGCCGGCGCGTACCGAAGCCTATAAATACTGGTTACAGGCAAATGGGGTAAGCGCCAACATCAGCACACACCCAAAAGACTTGTTAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGa                                                                                                                                                          >  1:314977/1‑251 (MQ=255)                                  aaTCTACGGTCAGCCGGCGCGTACCGAAGCCTATAAATACTGGTTACAGGCAAATGGGGTAAGCGCCAACATCAGCACACACCCAAAAGACTTGTTAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATAcga                                                                                                                                                                       >  1:26376/1‑229 (MQ=255)                                   aTCTACGGTCAGCCGGCGCGTACCGAAGCCTATAAATACTGGTTACAGGCAAATGGGGTAAGCGCCAACATCAGCACACACCCAAAAGACTTGTTAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTAc                                                                                                                                                  <  1:30571/251‑1 (MQ=255)                                               ccGGCGCGTACCGAAGCCTATAAATACTGGTTACAGGCAAATGGGGTAAGCGCCAACATCAGCACACACCCAAAAGACTTGGTAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCACTTGTGAAGCTCTACTCTGCTTatcat                                                                                                                                      <  1:442918/251‑1 (MQ=255)                                                         ccGAAGCCTATAAATACTGGTTACAGGCAAATGGGGTAAGCGCCAACATCAGCACACACCCAAAAGACTTGTTAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTatca                                                                                                                                       <  1:894063/240‑1 (MQ=255)                                                              gCCTATAAATACTGGTTACAGGCAAATGGGGTAAGCGCCAACATCAGCACACACCCAAAAGACTTGTTAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACgcgg                                                                                                                       >  1:825176/1‑251 (MQ=255)                                                                 tataAATACTGGTTACAGGCAAATGGGGTAAGCGCCAACATCAGCACACACCCAAAAGACTTGTTAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTAc                                                                                                                                                  <  1:88811/221‑1 (MQ=255)                                                                                   gCAAATGGGGTAAGCGCCAACATCAGCACACACCCAAAAGACTTGTTAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCAt                                                                                                   <  1:168404/250‑1 (MQ=255)                                                                                        tGGGGTAAGCGCCAACATCAGCACACACCCAAAAGACTTGTTAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCATccgccg                                                                                             >  1:338557/1‑251 (MQ=255)                                                                                          gggTAAGCGCCAACATCAGCACACACCCAAAAGACTTGTTAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATg                                                                                                                                                                                         <  1:373705/157‑1 (MQ=255)                                                                                          gggTAAGCGCCAACATCAGCACACACCCAAAAGACTTGTTAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATg                                                                                                                                                                                         <  1:810093/157‑1 (MQ=255)                                                                                                       catcagcacacacccaaaaGACTTGTTAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGc                                                                                                                                             >  1:399862/17‑188 (MQ=255)                                                                                                       catcagcacacacccaaaaGACTTGTTAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCATCCGCCGTTAAATAAGTTc                                                                                 >  1:127959/17‑248 (MQ=255)                                                                                                                   cccaaaaGACTTGTTAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTActc                                                                                                                                                >  1:888267/5‑173 (MQ=255)                                                                                                                   cccaaaaGACTTGTTAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGAc                                                                                                                           <  1:638895/190‑1 (MQ=255)                                                                                                                               tttAAAAAATAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATG‑AAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCATCCGCCGTTAAATAAGTTCTATTCAATTCGGGCTAAAAAACCACACg                                                     <  1:615130/250‑1 (MQ=255)                                                                                                                                  aaaaaaTAATGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACAAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCATCCGCCGTTAAATAAGTTCTATTCAATTCGGGCTAAAAAACCACACGaa                                                   <  1:654238/251‑1 (MQ=255)                                                                                                                                         aatGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCATCCGCCGTTAAATAAGTTCTATTCAATTCGGGCTAAAAAACCACACGAAACATTaa                                            <  1:545701/251‑1 (MQ=255)                                                                                                                                          atGTTAATATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCATCCGCCGTTAAATAAGTTCTATTCAATTCGGGCTAAAAAACCACACGAAACATTaaa                                           >  1:638875/1‑251 (MQ=255)                                                                                                                                            gttaaTATTACTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCATCCGCCGTTAAATAAGTTCTATTCAATTCGGGCTAAAAAACCACACGAAACATTAAAGa                                         >  1:19413/4‑251 (MQ=255)                                                                                                                                             taaaTATAACTTTCAGAAGAGGAGTGAAAAATAAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTACCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATAAATTACCCGGTGATACAAAAACCGCTTGTAAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGAAATGTCATCCGCCGTTAAATAAGTTCTATTCAATTCGGGCTAAAAAACCACACGAAACATTAAAGa                                         <  1:706607/248‑1 (MQ=255)                                                                                                                                                     aCTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCATCCGCCGTTAAATAAGTTCTATTCAAt                                                                         >  1:287343/1‑210 (MQ=255)                                                                                                                                                     aCTTTCAGAAGAGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGAATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCATCCGCCGTTAAATAAGTTCTATTCAAt                                                                         >  1:200640/1‑210 (MQ=255)                                                                                                                                                            gaagaGGAGTTAAAAATGAAAAAGCCCTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCATCCGCCGTTAAATAAGTTCTATTCAATTCGGGCTAAAAAACCACACGAAACATTAAAGAAACGTCGTAAtttttt                         >  1:745600/5‑251 (MQ=255)                                                                                                                                                                                      cTTTAAAATCGCTGTGATATGTCTTGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCATccgc                                                                                               <  1:821279/155‑1 (MQ=255)                                                                                                                                                                                                     gatatgtcttGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCATCCGCCGTTAAATAAGTTCTATTCAATTCGGGCTAAAAAACCACACGAAACATTAAAGa                                         >  1:333823/7‑194 (MQ=255)                                                                                                                                                                                                          gtcttGCCTTATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCATCCGCCGTTAAATAAGTTCTATTCAATTCGGGCTAAAAAACCACACGAAACATTAAAGAAACGTCGTAATTTTTTaaaat                    <  1:699793/209‑2 (MQ=255)                                                                                                                                                                                                               gccttATGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCATCCGCCGTTAAATAAGTTCTATTCAATTCGGGCTAAAAAAcc                                                          >  1:721412/4‑167 (MQ=255)                                                                                                                                                                                                                    aTGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCATCCGCCGTTAAATAAGTTCTATTCAATTc                                                                       >  1:709654/1‑149 (MQ=255)                                                                                                                                                                                                                    aTGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCATCCGCCGTTAAATAAGTTCTATTCAATTCGGGCTAAAAAACCACACGAAACATTAAAGAAAcgt                                    >  1:840205/1‑184 (MQ=255)                                                                                                                                                                                                                    aTGCAGTATGAGCCAGGTAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCATCCGCCGTTAAATAAGTTCTATTCAATTCGGGCTAAAAAACCACACGAAACATTAAAGAAACGTCGTAATTTTTTaaaattgtgtccaaattctaacg  <  1:811065/218‑20 (MQ=255)                                                                                                                                                                                                                                   ggtAAGTCATGCTGTAGATGAATTAACCGGTGATACGAAAACCGCTTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCATCCGCCGTTAAATAAGTTCTATTCAATTCGGGCTAAAAAACCACACGAAACATTAAAGAAACGTCGTAATTTTTTaaaat                    <  1:328687/183‑2 (MQ=255)                                                                                                                                                                                                                                               |                                                                                                                                                                                               TTTCTACTTTGCGCATCATGCAGATAGTATTGAAATCTACGGTCAGCCGGCGCGTACCGAAGCCTATAAATACTGGTTACAGGCAAATGGGGTAAGTGCCAATATCAGTACATATCAGAAAGACCTATTAAAAAATAATGTCAATATAACTTTCAGGAAAGGAGTTAAAAATGAAAAAGCCCTTTAAAATTGGTGTAATCTTTCTTGCTTTATGCAGTATGAGCCAAATAAGCCATGCGGTGGATGAATTAACCGGTGATACCAAAACCGCCTGTGAAGCTCTACTCTGCTTATCATCACCAAAAGACGCGGCGAAAACGCCGGAATGTCATCCGCCGTTAAATAAGTTCTATTCAATTCGGGCTAAAAAACCACACGAAACATTAAAGAAACGTCGTAACTTTTTAAAACTATGCCCGGATGCTAGTG  >  1/1454831‑1455259

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: ‑