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%	67.1 / NA	20	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 (6/14);  total (6/14)

ACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTGG  >  NC_000913/2563394‑2563653                                                                                                                               |                                                                                                                                      accaAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGaa                                                                                                                           >  1:222179/1‑139 (MQ=255)                    gAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATgg                                                                                                        <  1:202532/139‑1 (MQ=255)                                 tgATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTg                                                                                           <  2:490297/139‑1 (MQ=255)                                 tgATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTg                                                                                           <  2:464334/139‑1 (MQ=255)                                 tgATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTg                                                                                           <  2:265209/139‑1 (MQ=255)                                 tgATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTg                                                                                           <  2:106352/139‑1 (MQ=255)                                           cGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGaa                                                                                 <  2:250139/139‑1 (MQ=255)                                                     cTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTg                                                                                           >  1:217547/1‑119 (MQ=255)                                                     cTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTg                                                                                           <  2:217547/119‑1 (MQ=255)                                                       tCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAaggagg                                                                     >  2:385298/1‑139 (MQ=255)                                                        cAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAggagga                                                                    >  1:214575/1‑139 (MQ=255)                                                                              tcaaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCa                                              <  1:385298/139‑1 (MQ=255)                                                                               caaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCaa                                             <  1:436512/139‑1 (MQ=255)                                                                                                           tAAAGATTGTAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGGTGGTTTGCTGTGTGGATATGTGAAGGAGGACGCCATGAAACATTTGATGGCAATCTACCTGATGGCGCTGTCTGGTGtttc                 <  1:334447/139‑2 (MQ=255)                                                                                                           tAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGtttg                 <  2:214575/139‑1 (MQ=255)                                                                                                           tAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGtttg                 <  2:152176/139‑1 (MQ=255)                                                                                                             aaGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGtttgct               <  1:2253/139‑1 (MQ=255)                                                                                                              aGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGtttgctt              >  1:33633/1‑139 (MQ=255)                                                                                                                      ggTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATg      <  2:2571/139‑1 (MQ=255)                                                                                                                          aaaaTTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTgg  >  2:235024/1‑139 (MQ=255)                                                                                                                               |                                                                                                                                      ACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTGG  >  NC_000913/2563394‑2563653

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑