Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	589,934	0	T	G	40.8%	77.3 / 19.8	49	T341P (ACC→CCC)	nfrA	bacteriophage N4 receptor, outer membrane subunit
Reads supporting (aligned to +/- strand):  ref base T (1/28);  new base G (20/0);  total (21/28)
Fisher's exact test for biased strand distribution p-value = 7.43e-13
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATCAGTTGCCAGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTG‑TCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGTTAGCGCTGTATTTAGATAACAGA  >  NC_000913/589785‑590082                                                                                                                                                      |                                                                                                                                                        cATCAGTTGCCAGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTg                                                                                                                                                        <  2:584907/151‑1 (MQ=255)    cAGTTGCCAGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCg                                                                                                                                                     <  1:615227/151‑1 (MQ=255)    cAGTTGCCAGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGGTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGGCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGgggggggggggg                                                                                                                                                     >  1:319041/1‑149 (MQ=255)     aGTTGCCAGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATAAAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGggggggggggggg                                                                                                                                                    >  2:72069/1‑148 (MQ=255)     aGTTGCCAGGTTAGTTGATCCAGGCGGGGAAGATTTGCCGGTTTTTTGTGACACAGCAATAGTGCCCGACCCGGAGCTTCCGCCTTGTTAACGGGGGCCACGCTGGCAGCAAAACCCCCCCTAAACATTTCATTTGCGggggggggggggg                                                                                                                                                    >  1:385921/1‑148 (MQ=255)       ttGCCAGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATAAAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGggggggggggggggg                                                                                                                                                  >  1:698161/1‑146 (MQ=255)                tAGTTGATCCAGGCGGGTAAGATTTGGCCGTTTTTGCTGATACAGCAATCCTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAAAGCCCCTCAAGCATTTTATTGGCGggggggggggggggggggatttt                                                                                                                                          >  1:169452/1‑137 (MQ=255)                 aGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAACAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAAAGCTCCTCAAGCATTTCATTGGCGgggggggggggggggaggttt                                                                                                                                            >  1:254200/1‑136 (MQ=255)                      aTCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGAGGGGAGGGTGGCGAGCAGTTTTTGCGCTGcg                                                                                                                                   <  2:239158/151‑1 (MQ=255)                           ggCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGGAGttttt                                                                                                                                           >  2:53206/1‑138 (MQ=255)                              gggTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑g                                                                                                                          <  2:110854/151‑1 (MQ=255)                              gggTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑g                                                                                                                          <  1:68113/151‑1 (MQ=255)                                   aGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACctt                                                                                                                     <  2:631085/151‑1 (MQ=255)                                     aTTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGCAGGTTTTTCGCTGCGTCGTACT‑GACcctc                                                                                                                    >  2:988771/1‑150 (MQ=255)                                       ttGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGGGGCGAGCAGGTTTTTCGGCGCGCCGTGCT‑GACCCTtttt                                                                                                                 >  2:691401/1‑151 (MQ=255)                                           cGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AAc                                                                                                            <  1:116636/151‑1 (MQ=255)                                            ggTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACa                                                                                                           <  2:556966/151‑1 (MQ=255)                                                cTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGCAGGTTTTTCGCTGCGTCGTACT‑GACCTTCtttt                                                                                                                >  2:494835/1‑143 (MQ=255)                                                      gATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGAGCAGGTTTTTCGCTGCGTCGTACT‑GACCTTCTTTT‑TAAAACAcc                                                                                                      >  1:770636/1‑146 (MQ=255)                                                      gATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGt                                                                                                   <  1:967886/149‑1 (MQ=255)                                                       aTACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGCAGTTTTTTCGCTGCGGCGTACT‑GACCTTTTTTT‑TAAAGAAcc                                                                                                      >  2:560256/1‑145 (MQ=255)                                                         aCAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGt                                                                                              <  1:364496/151‑1 (MQ=255)                                                          cAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTc                                                                                             <  1:955588/151‑1 (MQ=255)                                                            gCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTGCGGGTCGCCCCGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTcg                                                                                            <  1:687038/150‑1 (MQ=255)                                                             cAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGGGGGGAGGAGGTTTTTCGCTGCGTCGTACT‑GAACTTTTTTT‑AACAACACCCGGAGCGgcgc                                                                                           >  2:556669/1‑150 (MQ=255)                                                               aTCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGAGAAGATTTTTCGACGCCGCGCACT‑TACCTTCCTTT‑TACAGCACCCGGAGCGTCGCGcc                                                                                        >  1:95009/1‑151 (MQ=255)                                                                    gCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGCAGTTTTTTCGCCGCGGCGTACT‑GACCTTCTTTT‑TACAACACCGGTAGCGTCGCGGcacca                                                                                    >  1:412669/1‑150 (MQ=255)                                                                    gCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTCGCGCcaacaa                                                                                   <  2:46341/151‑1 (MQ=255)                                                                     ccAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTCGCGCcaacaa                                                                                   <  1:588758/150‑1 (MQ=255)                                                                       aGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGAGCAGGTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑TACAGCACCGGGAGCGTCGCGCcaacaa                                                                                   >  2:728542/1‑148 (MQ=255)                                                                         aCGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGGGCCGTTTTTTCGCCTCGGCGGAAT‑CACCTTCTTTT‑TAAAACACCCGGAGCGTCCCGCccaca                                                                                    >  2:1014954/1‑145 (MQ=255)                                                                           gCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTCGCGCCAACAACATACTg                                                                            <  1:194653/151‑1 (MQ=255)                                                                             agagCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGAGGAGTATTTGCGCCGCGTCGGACT‑TAACTTCTTTT‑TAAAGCAACGGCAGGGGCGCGCCAacaacaaa                                                                               >  1:648580/1‑144 (MQ=255)                                                                             agagCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTCGCGCCAACAACATACTGGc                                                                          <  1:134924/151‑1 (MQ=255)                                                                                  ttCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGGGCAGTTTTTTCGCTGCGTCGTACT‑GACCTTCTTTT‑TACAGCACCGGGAGCGGCGCGCCAACAACATAATGGCggg                                                                       >  2:837092/1‑148 (MQ=255)                                                                                    cAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGAGCAGGTTTTTGGCTGCGGCGTACT‑GAACTTCTTTT‑TAAAGCAACCGGGGCGGCGCGCCCAAAACAAACcggcgg                                                                        >  1:105925/1‑146 (MQ=255)                                                                                     aGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGAGCAGGTTTTGGGCGGCGGCGGGCTGGACCTCTTTTT‑AACACAACCGG‑AGAGTCGCGCCAAAAACAAACTCGCGGGTg                                                                     >  1:40199/1‑148 (MQ=255)                                                                                     aGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGGGCAGTTTTTTCGCTGCGGCGTACT‑GACCTTCTTTT‑TACAACACCCGGAGCGGCGCGCCCACAACATACTGGCggg                                                                       >  2:549708/1‑145 (MQ=255)                                                                                        cTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGGGGCGAGCAGGTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑TACAGCACCGGTAGCGTCGCGCCAACAACAAACTGGCgggggt                                                                    >  2:175424/1‑142 (MQ=255)                                                                                         ttGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGGGGGGAGTTTTTTTGCTGCGTCGGACT‑TACCCTCTTTTAAACGGAACCGG‑AGTCTCGCGCCAacaacaatcttccgg                                                                        >  1:552808/1‑132 (MQ=255)                                                                                             tACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑TACAACACCCGTAGCGTCGCGCCAACAACATAATGGCgggtttgggggaaaac                                                          >  2:109109/1‑137 (MQ=255)                                                                                                       cACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTG‑TCGGCAAACTGTACCGTATaa                                               <  2:663889/151‑1 (MQ=255)                                                                                                          gCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTG‑TCGGCAAACTGTACCGTATAATTc                                            <  2:313518/151‑1 (MQ=255)                                                                                                          gCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTG‑TCGGCAAACTGTACCGTATAATTc                                            <  2:924344/151‑1 (MQ=255)                                                                                                           cTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGGGGGGGGCGAGCAGGTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑TACAGCACCGGGAGCGTCGCGCCAACAACATACTGGCGGGTGTTTGGCAAACttaccccataa                                                >  2:684574/1‑137 (MQ=255)                                                                                                                     aaCGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTG‑TCGGCAAACTGTACCGTATAATTCGCCAACGCCt                                  <  1:1004313/150‑1 (MQ=255)                                                                                                                     aaCGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTG‑TCGGCAAACTGTACCGTATAATTCGCCAACGCCTg                                 <  2:524199/151‑1 (MQ=255)                                                                                                                     aaCGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTG‑TCGGCAAACTGTACCGTATAATTCGCCAACGCCTg                                 <  1:556656/151‑1 (MQ=255)                                                                                                                              cAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTG‑TCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGtt                        <  1:553696/151‑1 (MQ=255)                                                                                                                              cAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTGTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTG‑TCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGtt                        <  2:151317/151‑1 (MQ=255)                                                                                                                                     ttCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTG‑TCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGTTAGCGCt                  <  1:367357/150‑1 (MQ=255)                                                                                                                                        aTTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTG‑TCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGTTAGCGCTGTAt              <  1:784895/151‑1 (MQ=255)                                                                                                                                              ggggAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTG‑TTGGGCAAATGTACCCGATAATTTACCAAACCCCGCAAGGGGGTAGGGCTGGAttt            >  1:714858/1‑147 (MQ=255)                                                                                                                                                   gggTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTG‑TCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGTTAGCGCTGTATTTAGATAACAg   <  1:183303/151‑1 (MQ=255)                                                                                                                                                    ggTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTG‑TCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGTTAGCGCTGTATTTAGATAACAGa  <  2:404852/151‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                        CATCAGTTGCCAGGTTAGTTGATCCAGGCGGGTAAGATTTGCCGGTTCTTGCTGATACAGCAATCGTGCCAGACGCAGAGCTTCAGCCTTGTTACGGGTCGCCACGCTGACAGCATAACGCTCCTCAAGCATTTCATTGGCGGGGAGGGTGGCGAGCAGTTTTTGCGCTGCGTCGTACT‑GACCTTCTTTT‑AACAGCACCGGTAGCGTCGCGCCAACAACATACTGGCGGTTG‑TCGGCAAACTGTACCGTATAATTCGCCAACGCCTGAACGGGGTTAGCGCTGTATTTAGATAACAGA  >  NC_000913/589785‑590082

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑