Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,564,482	T→C	intergenic (+110/‑41)	yffR → / → yffS	CPZ‑55 prophage; uncharacterized protein YffR/CPZ‑55 prophage; uncharacterized protein YffS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,564,482	0	T	C	100.0%	158.6 / NA	42	intergenic (+110/‑41)	yffR/yffS	CPZ‑55 prophage; uncharacterized protein YffR/CPZ‑55 prophage; uncharacterized protein YffS
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (21/21);  total (21/21)

GGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCTCAACGTGGGGCCAAATGCGAGGAGAT  >  NC_000913/2564346‑2564617                                                                                                                                         |                                                                                                                                        ggtagAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTaa                                                                                                                                      <  1:437237/140‑1 (MQ=255)      agTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTcc                                                                                                                                 >  2:387790/1‑140 (MQ=255)          tttGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAAt                                                                                                                             <  1:584408/140‑1 (MQ=255)                aaaCGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTc                                                                                                                       <  2:635834/140‑1 (MQ=255)                aaaCGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTc                                                                                                                       <  1:409181/140‑1 (MQ=255)                  aCGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTa                                                                                                                     <  2:408764/140‑1 (MQ=255)                          gattgCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATgg                                                                                                             <  1:441893/140‑1 (MQ=255)                                 aaTAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATaa                                                                                                      >  2:594891/1‑140 (MQ=255)                                      caacaaCTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATc                                                                                                 <  1:504547/140‑1 (MQ=255)                                           acTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAg                                                                                            >  1:494531/1‑140 (MQ=255)                                               aacaacCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTAc                                                                                        >  2:424864/1‑140 (MQ=255)                                               aacaacCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTAc                                                                                        >  1:89987/1‑140 (MQ=255)                                                    ccAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAAt                                                                                   >  1:257014/1‑140 (MQ=255)                                                       aTACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCa                                                                                                >  2:476004/1‑124 (MQ=255)                                                       aTACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCa                                                                                                <  1:476004/124‑1 (MQ=255)                                                             ccGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTg                                                                          >  1:14227/1‑140 (MQ=255)                                                              cGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGc                                                                         >  1:78346/1‑140 (MQ=255)                                                              cGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGc                                                                         >  1:193181/1‑140 (MQ=255)                                                               ggCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCg                                                                        <  2:518854/140‑1 (MQ=255)                                                               ggCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCg                                                                        >  2:449252/1‑140 (MQ=255)                                                               ggCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCg                                                                        <  1:449252/140‑1 (MQ=255)                                                                 ccccTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGAc                                                                      <  2:193181/140‑1 (MQ=255)                                                                    cTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATc                                                                   <  2:89987/140‑1 (MQ=255)                                                                             ttttttGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGgc                                                          <  1:198447/140‑1 (MQ=255)                                                                                       tCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATgg                                                >  1:12675/1‑140 (MQ=255)                                                                                        cTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGa                                               <  2:78346/140‑1 (MQ=255)                                                                                          gCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAg                                             <  2:12675/140‑1 (MQ=255)                                                                                          gCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAg                                             <  1:454875/140‑1 (MQ=255)                                                                                            gTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGa                                           <  2:14227/140‑1 (MQ=255)                                                                                            gTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGa                                           <  1:594891/140‑1 (MQ=255)                                                                                            gTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGa                                           <  2:494531/140‑1 (MQ=255)                                                                                                     cccTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAg                                  >  1:451192/1‑140 (MQ=255)                                                                                                      ccTTCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAgg                                 <  1:145496/140‑1 (MQ=255)                                                                                                        ttCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGgc                               >  2:167444/1‑140 (MQ=255)                                                                                                        ttCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGgc                               >  2:577649/1‑140 (MQ=255)                                                                                                         tCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGa                                               >  1:540350/1‑123 (MQ=255)                                                                                                         tCCGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGa                                               <  2:540350/123‑1 (MQ=255)                                                                                                           cGTTACGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCt                            >  2:245126/1‑140 (MQ=255)                                                                                                                cGCTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCTCAACg                       >  1:175576/1‑140 (MQ=255)                                                                                                                  cTTACCCTCCACCAATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCTCAACGTg                     >  1:461434/1‑140 (MQ=255)                                                                                                                           caccaATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCTCAACGTGGGGCCAAAt            >  2:122304/1‑140 (MQ=255)                                                                                                                              caATACGCGTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCTCAACGTGGGGCCAAATGCg         <  2:451192/140‑1 (MQ=255)                                                                                                                                     cgTGCTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCTCAACGTGGGGCCAAATGCGAGGAGAt  >  1:648933/1‑140 (MQ=255)                                                                                                                                         |                                                                                                                                        GGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCTCAACGTGGGGCCAAATGCGAGGAGAT  >  NC_000913/2564346‑2564617

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑