Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	589,934	0	T	G	42.0%	88.6 / 12.6	50	T341P (ACC→CCC)	nfrA	bacteriophage N4 receptor, outer membrane subunit
Reads supporting (aligned to +/- strand):  ref base T (2/27);  new base G (21/0);  total (23/27)
Fisher's exact test for biased strand distribution p-value = 3.76e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCATCAGTTGCCAGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATAC‑TG‑GCGGTTGTCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGTTAGCGCTGTATTTAGAT  >  NC_000913/589784‑590076                                                                                                                                                       |                                                                                                                                                 gCATCAGTTGCCAGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGt                                                                                                                                                  <  2:854204/151‑1 (MQ=255)   aTCAGTTGCCAGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTgg                                                                                                                                                <  2:759945/151‑1 (MQ=255)     cAGTTGCCAGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGc                                                                                                                                               <  1:254238/150‑1 (MQ=255)     cAGTTGCCAGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGGTCTTGCTGATACAGCAATCGTGCCCGGCGCAGAGCGTCAGCCTTGGTAAGGGGCGCCACGCTGACAGCATAAAGCTCCTAAAGCATTTCATTgggggggggggggggg                                                                                                                                              >  2:442770/1‑149 (MQ=255)             aGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGttt                                                                                                                                      <  2:676636/151‑1 (MQ=255)             aGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATAAAGCAATCGTGCCAAAAGCAGAGGTTCAGCCCTGTTACGGGTCGCCACGCTGACAGCATAAAGCTCCTCAAGCATTTCCTTGGCGggggggggggggcg                                                                                                                                            >  1:877691/1‑141 (MQ=255)              ggTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGtttt                                                                                                                                     <  2:175680/151‑1 (MQ=255)               gTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGttttt                                                                                                                                    <  1:1054449/151‑1 (MQ=255)               gTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGttttt                                                                                                                                    <  1:888501/151‑1 (MQ=255)                     tGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCCTTTCATTGGCGggggggggggggggggagttttt                                                                                                                                   >  1:349049/1‑133 (MQ=255)                     tGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCt                                                                                                                               <  1:703580/150‑1 (MQ=255)                      gATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGATg                                                                                                                              <  1:16445/150‑1 (MQ=255)                          cAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGGCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGAGGAGGTTTTTGGCTCcgt                                                                                                                           >  1:677139/1‑149 (MQ=255)                           aGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGGAGgttttttgcctgggcg                                                                                                                         >  1:616130/1‑139 (MQ=255)                            ggCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTa                                                                                                                       <  1:297975/151‑1 (MQ=255)                                 gTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGAGGAGGGTTTTCGCTCCGGCCTTCTGAc                                                                                                                  >  2:843684/1‑151 (MQ=255)                                  tAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGGGGGGGGCAGGTTTTTCGCTGCGTCGGACTGAcc                                                                                                                 >  1:400539/1‑151 (MQ=255)                                   aaGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGGGGAGATTTTGTGGTGCGGCGTACTGAcc                                                                                                                 >  2:825716/1‑150 (MQ=255)                                        ttGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGCAGTTTTTTCGCTGCGTCGTGCTGACCTTCttt                                                                                                           >  2:166464/1‑151 (MQ=255)                                         tGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGGCGGTTTTTCGCTGCCCCGTACttgccctccttt                                                                                                          >  2:893532/1‑140 (MQ=255)                                          gCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGGGGGGAGGAGGTTTTTCGCTGCGGCGCTCTTACCTTCttttt                                                                                                         >  2:928650/1‑150 (MQ=255)                                           ccGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGAGCAGGTTTTGCGCTGCGCCCTACTGACCTTCtttt                                                                                                          >  1:969580/1‑149 (MQ=255)                                            cGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGAGCAGTTTTTTCGCTGCGTCGTACTGACCTTCttttta                                                                                                        >  1:837079/1‑148 (MQ=255)                                             ggTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACa                                                                                                      <  2:641845/151‑1 (MQ=255)                                             ggTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACa                                                                                                      <  2:12755/151‑1 (MQ=255)                                                  ttGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGAGGAGGTTTTTCGCCGCGTCGTACTTGCCTTCTTTTTAAAACAcc                                                                                                 >  2:640818/1‑151 (MQ=255)                                                      tGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGCAGGTTTTTCGCTTCGTCGTACTTACCTTTTTTTTACAGCACCgg                                                                                               >  1:938483/1‑149 (MQ=255)                                                        aTACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGCCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGc                                                                                           <  2:1053157/151‑1 (MQ=255)                                                           cAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTc                                                                                        <  2:868968/151‑1 (MQ=255)                                                            aGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGAGGCGGTTTTTTGCTGCGTCGTACTTACCTTCTTTTTAAAACAcccggag                                                                                            >  2:19187/1‑141 (MQ=255)                                                            aGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGAGCAGTTTTTTCGCTGCGTCGTACTGACCCTCTTTTTAAAACACCGGGAGCg                                                                                          >  2:979471/1‑148 (MQ=255)                                                             gCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTcgc                                                                                      <  1:261174/151‑1 (MQ=255)                                                             gCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTcgc                                                                                      <  1:934150/151‑1 (MQ=255)                                                               aaTCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGGAGTTTTTTCGCTGCGGCGGACTGAACTTCTTTTTAAAACAACGGGAgcggcg                                                                                       >  1:370420/1‑148 (MQ=255)                                                                 tCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGGAGGTTTTTTGCTGCGTCGTACTGACCTTTTTTTTACAGCACCGGGAGCGGCGCGcc                                                                                   >  1:521056/1‑150 (MQ=255)                                                                     gCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGAGCAGTTTTTTCGCTGCGTCGTACTGACCTTCTTTTTACAGCACCGGGAGCGTCGCGCcaa                                                                                 >  1:841257/1‑148 (MQ=255)                                                                            gCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGTAGCCGGTTTTTCGTAGGGCAGGACTGGAATTCTTTTTACAACACCGGCGACGTCGCGCCAacaaca                                                                            >  2:550284/1‑146 (MQ=255)                                                                                    tCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATAC‑TG‑GCGGtt                                                               <  2:551083/149‑1 (MQ=255)                                                                                    tCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGGGGCGGGCAGGTTTTTCGCCGCGTCGCCCTGACCTTCTTTTTACAACACCCGTGGGGTCGCGcccaaaa                                                                              >  1:843316/1‑131 (MQ=255)                                                                                      aGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCACCAACATAC‑TG‑GCGGTTGTCg                                                           <  2:950428/151‑1 (MQ=255)                                                                                          ttGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGCAGGTTTTTCGCTGCGTCGTGCTGACCTTCTTTTTACAAGACCGGGAGCGGCGCGCCAACAAAATAC‑TG‑GCgggatggtgg                                                         >  1:957723/1‑141 (MQ=255)                                                                                            gTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATAC‑TG‑GCGGTTGTCGGCAAAc                                                     <  2:628278/151‑1 (MQ=255)                                                                                            gTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATAC‑TG‑GCGGTTGTCGGCAAAc                                                     <  2:349047/151‑1 (MQ=255)                                                                                                      gCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATAC‑TG‑GCGGTTGTCGGCAAACTGTACCGtat                                           <  2:562737/151‑1 (MQ=255)                                                                                                       ccACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATAC‑TG‑GCGGTTGTCGGCAAACTGTACCGtata                                          <  2:813091/151‑1 (MQ=255)                                                                                                             tGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGGGCCGATTTTTTGGGGCGTTGTACTTCACCTCTTTTTCCAGCAACTCTAACGCTGCGCCCACAACATACGTGCGCGGTTGTTgggcctc                                                     >  1:379087/1‑131 (MQ=255)                                                                                                              gACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATAC‑TG‑GCGGTTGTCGGCAAACTGTACCGTATAATTCGcc                                   <  2:110760/151‑1 (MQ=255)                                                                                                                      aaCGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATAC‑TG‑GCGGTTGTCGGCAAACTGTACCGTATAATTCGCCAACGCCt                            <  1:999070/150‑1 (MQ=255)                                                                                                                                  gCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATAC‑TG‑GCGGTTGTCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGTTAgc               <  2:389477/151‑1 (MQ=255)                                                                                                                                       tCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATAC‑TG‑GCGGTTGTCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGTTAGCGCTg           <  1:6298/150‑1 (MQ=255)                                                                                                                                             gCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATAC‑TG‑GCGGTTGTCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGTTAGCGCTGTATTTAg    <  1:282233/151‑1 (MQ=255)                                                                                                                                               ggggAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATAC‑TG‑GCGGTTGTCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGTTAGCGCTGTATTTAGAt  <  1:890985/151‑1 (MQ=255)                                                                                                                                                 ggAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATAC‑TG‑GCGGTTGTCGGGAAACTGTACCGTATAAATTGCCAACGCCCGAAACGGGGTAGCGCTGTATTTAGAt  >  1:697313/1‑149 (MQ=255)                                                                                                                                                 ggAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATAC‑TG‑GCGGTTGTCGGCAAAATGTACCCGATAATTTGCCCACGCCCGGACGGGGGTTGGGCTGTAttt      >  1:327156/1‑145 (MQ=255)                                                                                                                                                       |                                                                                                                                                 GCATCAGTTGCCAGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATAC‑TG‑GCGGTTGTCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGTTAGCGCTGTATTTAGAT  >  NC_000913/589784‑590076

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑