Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,563,520	G→T	intergenic (+403/‑72)	yffP → / → yffQ	CPZ‑55 prophage, uncharacterized protein/CPZ‑55 prophage, uncharacterized protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,563,520	0	G	T	100.0%	229.9 / NA	66	intergenic (+403/‑72)	yffP/yffQ	CPZ‑55 prophage, uncharacterized protein/CPZ‑55 prophage, uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (31/35);  total (31/35)

ACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTGG  >  NC_000913/2563388‑2563653                                                                                                                                     |                                                                                                                                      aCTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACgg                                                                                                                                 >  2:581844/1‑139 (MQ=255) aCTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACgg                                                                                                                                 >  1:1091353/1‑139 (MQ=255)       accaAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCCTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGaa                                                                                                                           <  2:1130175/139‑1 (MQ=255)         caAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGt                                                                                                                         <  2:795375/139‑1 (MQ=255)           aaGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTgg                                                                                                                       <  1:456853/139‑1 (MQ=255)                aacaaGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTa                                                                                                                  <  2:32866/139‑1 (MQ=255)                aacaaGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTa                                                                                                                  <  2:134864/139‑1 (MQ=255)                 acaaGATGGGAGGTTAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGt                                                                                                                                <  1:751961/124‑1 (MQ=255)                 acaaGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGt                                                                                                                                >  2:751961/1‑124 (MQ=255)                     gATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGt                                                                                                             <  2:1091353/139‑1 (MQ=255)                     gATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGt                                                                                                             <  2:1053292/139‑1 (MQ=255)                       tGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCCACGAATGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCATTACtttgga                                                                                                           >  1:285895/1‑134 (MQ=255)                        gggAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGAt                                                                                                          >  1:945176/1‑139 (MQ=255)                            ggTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTa                                                                                                      >  2:10003/1‑139 (MQ=255)                             gTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTaa                                                                                                     <  2:438200/139‑1 (MQ=255)                             gTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTaa                                                                                                     >  1:438200/1‑139 (MQ=255)                                aaTTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGt                                                                                                  >  1:1041127/1‑139 (MQ=255)                                    ttGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGt                                                                                              <  2:438697/139‑1 (MQ=255)                                     tgtgATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGtt                                                                                             >  1:395351/1‑139 (MQ=255)                                       tgATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTg                                                                                           <  2:945176/139‑1 (MQ=255)                                          tGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTg                                                                                        >  1:376655/1‑139 (MQ=255)                                            cAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTa                                                                                      <  1:581844/139‑1 (MQ=255)                                               aTCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTg                                                                                   <  1:547698/139‑1 (MQ=255)                                                tCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTT‑GTTTGCTGTATTGaa                                                                                 <  2:347291/139‑1 (MQ=255)                                                 cGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGt                                                                                                                                <  1:917429/92‑1 (MQ=255)                                                 cGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGt                                                                                                                                >  2:917429/1‑92 (MQ=255)                                                      tttCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGt                                                                                                                                <  2:1145069/87‑1 (MQ=255)                                                      tttCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGt                                                                                                                                >  1:1145069/1‑87 (MQ=255)                                                         cccTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTgg                                                                                                                       <  2:841020/93‑1 (MQ=255)                                                         cccTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTgg                                                                                                                       >  1:841020/1‑93 (MQ=255)                                                                            tAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGt                                                                                                                                <  1:1168315/65‑1 (MQ=255)                                                                            tAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGt                                                                                                                                >  2:1168315/1‑65 (MQ=255)                                                                               ttCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGc                                                                 <  2:481256/125‑1 (MQ=255)                                                                               ttCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGc                                                                 >  1:481256/1‑125 (MQ=255)                                                                                    tcaaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCa                                              <  1:10003/139‑1 (MQ=255)                                                                                        cGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTaaa                                                                                                                                    <  1:344540/49‑1 (MQ=255)                                                                                        cGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTaaa                                                                                                                                    >  2:344540/1‑49 (MQ=255)                                                                                        cGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTg                                                                                   <  2:531786/98‑1 (MQ=255)                                                                                        cGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTg                                                                                   >  1:531786/1‑98 (MQ=255)                                                                                              gCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGa                                    >  1:1082311/1‑139 (MQ=255)                                                                                                  ttCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTaa                                                                                                     >  2:74853/1‑70 (MQ=255)                                                                                                  ttCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTaa                                                                                                     <  1:74853/70‑1 (MQ=255)                                                                                                  ttCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGt                                >  1:222661/1‑139 (MQ=255)                                                                                                            caaAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACt                                                                               <  1:449237/82‑1 (MQ=255)                                                                                                            caaAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACt                                                                               >  2:449237/1‑82 (MQ=255)                                                                                                              aaaTAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGgtgt                    <  2:222661/139‑1 (MQ=255)                                                                                                               aaTAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGttt                                                                                            <  1:425831/66‑1 (MQ=255)                                                                                                               aaTAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGttt                                                                                            >  2:425831/1‑66 (MQ=255)                                                                                                               aaTAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTg                                                                                           <  2:883011/67‑1 (MQ=255)                                                                                                               aaTAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTg                                                                                           >  1:883011/1‑67 (MQ=255)                                                                                                                 tAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGtttg                 <  2:554766/139‑1 (MQ=255)                                                                                                                  aaaGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGtttgc                <  2:1041127/139‑1 (MQ=255)                                                                                                                    aGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCaa                                             <  1:299813/108‑1 (MQ=255)                                                                                                                    aGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCaa                                             >  2:299813/1‑108 (MQ=255)                                                                                                                      aTGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAAc                                                                                >  2:965694/1‑71 (MQ=255)                                                                                                                      aTGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAAc                                                                                <  1:965694/71‑1 (MQ=255)                                                                                                                       tGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGtttgctttgc           >  2:100189/1‑139 (MQ=255)                                                                                                                         ggAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTg                                                                                           >  2:284678/1‑57 (MQ=255)                                                                                                                         ggAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTg                                                                                           <  1:284678/57‑1 (MQ=255)                                                                                                                         ggAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTg                                     <  1:219001/111‑1 (MQ=255)                                                                                                                         ggAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTg                                     >  2:219001/1‑111 (MQ=255)                                                                                                                         ggAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAg         >  2:247451/1‑139 (MQ=255)                                                                                                                         ggAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAg         >  2:1106493/1‑139 (MQ=255)                                                                                                                         ggAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAg         >  1:299152/1‑139 (MQ=255)                                                                                                                            ggTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATg      <  2:1082311/139‑1 (MQ=255)                                                                                                                                aaaaTTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTgg  <  2:483894/139‑1 (MQ=255)                                                                                                                                     |                                                                                                                                      ACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTGG  >  NC_000913/2563388‑2563653

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑