Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	589,934	0	T	G	43.5%	78.8 / 17.8	46	T341P (ACC→CCC)	nfrA	bacteriophage N4 receptor, outer membrane subunit
Reads supporting (aligned to +/- strand):  ref base T (1/25);  new base G (20/0);  total (21/25)
Fisher's exact test for biased strand distribution p-value = 3.74e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCAGTTGCCAGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTGTCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGTTAGCGCTGTATTTAGATAA  >  NC_000913/589787‑590078                                                                                                                                                    |                                                                                                                                                 tCAGTTGCCAGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGGTTTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGACTTGTTACGGGTGGCCACGCCGACAGCATAACGCCCCTCCAGCATTTCATTGGCGgggggggggg                                                                                                                                                >  2:273143/1‑150 (MQ=255)      tGCCAGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGc                                                                                                                                           <  2:78758/150‑1 (MQ=255)         cAGGTTAGTTGATCCAGGCGGGGAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCCGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGgggggggggggggg                                                                                                                                            >  1:957288/1‑142 (MQ=255)           ggTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGgggggggggggggggaggttt                                                                                                                                     >  2:803842/1‑140 (MQ=255)              tAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGggggggggggggggggggtttt                                                                                                                                    >  1:409278/1‑137 (MQ=255)              tAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGAgggggttttt                                                                                                                                   >  2:367001/1‑141 (MQ=255)                  tGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCt                                                                                                                               <  1:305979/150‑1 (MQ=255)                    aTCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGcg                                                                                                                            <  1:135727/151‑1 (MQ=255)                    aTCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGGCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGgggggggggggggggggggttt                                                                                                                                    >  1:607086/1‑131 (MQ=255)                    aTCCAGGCGGGTAAGATTTGCCGGGTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCCGACAGCATAACGCTCCTCAAGCATTTCATTGGCGggggggggggggggggggtttt                                                                                                                                    >  1:539083/1‑131 (MQ=255)                       cAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGCAGgtttt                                                                                                                                    >  2:1009975/1‑140 (MQ=255)                       cAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGcgtcg                                                                                                                         <  1:1004866/151‑1 (MQ=255)                          gCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGGAGGTTTTGTGCTGCGGCGTa                                                                                                                       >  1:1012211/1‑150 (MQ=255)                           cGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGGGCAGGTTTTTCGCCgcggcggcc                                                                                                                      >  2:381958/1‑147 (MQ=255)                            gggTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGAGCAGTTTTTTCGCTGCGTCGTTCt                                                                                                                     >  2:244862/1‑150 (MQ=255)                                 aGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGGGCAGGTTTTTCGGTGCGTCGTACTGACctt                                                                                                               >  2:405147/1‑151 (MQ=255)                                   aTTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGGGGGGGGCAATTTTTGCGCTTCGGCGTAAAAACcttct                                                                                                             >  2:74453/1‑151 (MQ=255)                                       gCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCtttt                                                                                                          <  2:42630/150‑1 (MQ=255)                                            ttCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGGGGCGGGCAGGTTTTTGGCTTCGTCGGACTGACCTTCTTTTTACa                                                                                                      >  2:575591/1‑149 (MQ=255)                                              cTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGCCGGTTTTTCGCTGCGGCGTACTGACCCTCTTTTTACAGc                                                                                                    >  1:823452/1‑149 (MQ=255)                                              cTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGAGCAGTTTTTTCGCTGCGTCGTACTGACCTTCTTTTTacaaca                                                                                                   >  1:214157/1‑150 (MQ=255)                                               ttGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGGCGGTTTTTCGCCGGGGCGTATTGACCCTCtttttaa                                                                                                       >  1:879681/1‑142 (MQ=255)                                               ttGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGAGGAGGTTTTGCGCTGCGTCGTACTGACCTTCTTTTTACAGCAcc                                                                                                 >  1:319158/1‑151 (MQ=255)                                                 gCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCg                                                                                                <  1:702474/150‑1 (MQ=255)                                                    gATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTa                                                                                             <  1:862256/150‑1 (MQ=255)                                                         aGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTcg                                                                                       <  2:870098/151‑1 (MQ=255)                                                          gCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTcgc                                                                                      <  2:402952/151‑1 (MQ=255)                                                               cGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCca                                                                                  <  2:536924/150‑1 (MQ=255)                                                                        cGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGAGCAGGTTTTTCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGGAGCGTCGCGCCCacaaca                                                                            >  2:371932/1‑147 (MQ=255)                                                                         gCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTg                                                                       <  2:878324/151‑1 (MQ=255)                                                                           agagCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGAGCAGTATTTTCGCTGCGTCGTACTGACCTTCTTTTTACAGCACCGGGAGCGTCGCGCCAACAACATACTg                                                                       >  2:869000/1‑149 (MQ=255)                                                                             agCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGAGCAGGTTTTGTGCTGCGTCGGACTGGCCTTCTTTTTAAAGCACCGGGAGGGTCGCGCCCACAACATAATgggcg                                                                   >  1:355296/1‑148 (MQ=255)                                                                              gCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGGGGCGGTTTTGCGCTGCGGCGTAATGACCTTTTTTTTACAGCACCGGGAGCGTCGCGCCCAAAACATACTGGCg                                                                    >  1:148422/1‑149 (MQ=255)                                                                                   aGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTGTCg                                                             <  2:65971/151‑1 (MQ=255)                                                                                   aGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTGTCg                                                             <  2:975218/151‑1 (MQ=255)                                                                                       ttGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGAGCAGTTTTTTCGCTGCGTCGTACTGACCTTCTTTTTACAGCACCCGGAGCGTCGCGCCCACAACATACTGGCgggttgtgg                                                            >  2:172196/1‑141 (MQ=255)                                                                                       ttGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGGGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTTACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCggg                                                                  >  2:554001/1‑141 (MQ=255)                                                                                        tGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTTACAGCACCGGGAGCGGCGCGCCCACAAAAAACTTGCgggt                                                                 >  2:439974/1‑140 (MQ=255)                                                                                           tACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTGTCGGCAAACt                                                      <  2:868909/150‑1 (MQ=255)                                                                                            aCGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTGTCGGCAAACTg                                                     <  2:259113/150‑1 (MQ=255)                                                                                            aCGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTGTCGGCAAACTGt                                                    <  2:489986/151‑1 (MQ=255)                                                                                                    ccACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTGTCGGCAAACTGTACCGtata                                            <  2:666858/151‑1 (MQ=255)                                                                                                    ccACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGGGGCGAGCAGTTTTTTCGCTGCGTCGTACTGACCTTCTTTTTACAGCACCGGGAGCGTCGCGCCCACAACAAACTGGCGGGTGTTgggcaaaac                                                     >  2:357786/1‑135 (MQ=255)                                                                                                            aCAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTGTCGGCAAACTGTACCGTATAATTCGCCa                                    <  1:244278/151‑1 (MQ=255)                                                                                                             cAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTGTCGGCAAACTGTACCGTATAATTCGCCa                                    <  1:970200/150‑1 (MQ=255)                                                                                                               gCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTATCAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTGTCGGCAAACTGTACCGTATAATTCGCCAACg                                 <  1:618604/151‑1 (MQ=255)                                                                                                               gCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTGTCGGCAAACTGTACCGTATAATTCGCCAACg                                 <  2:398725/151‑1 (MQ=255)                                                                                                                     cGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTGTCGGCAAACTGTACCGTATAATTCGCCAACGCCTGaa                           <  2:613313/151‑1 (MQ=255)                                                                                                                                    tCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTGTCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGTTAGCGCTg             <  1:1009829/150‑1 (MQ=255)                                                                                                                                         ggCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTGTCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGTTAGCGCTGTAttt        <  1:145594/150‑1 (MQ=255)                                                                                                                                              ggAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTGTCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGTTAGCGCTGTATTTAGATaa  <  2:539174/151‑1 (MQ=255)                                                                                                                                               gAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTTTTGGCAAACTGTACCGGATAAATTTCCCACGCCCGAAAGGGGGTTGGGCTGTAttt        >  2:455273/1‑144 (MQ=255)                                                                                                                                                    |                                                                                                                                                 TCAGTTGCCAGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACTGACCTTCTTTTAACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTGTCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGTTAGCGCTGTATTTAGATAA  >  NC_000913/589787‑590078

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: ‑