Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,604,237	0	C	T	41.5%	64.8 / 22.5	53	S64L (TCG→TTG)	lsrD	autoinducer 2 import system permease protein
Reads supporting (aligned to +/- strand):  ref base C (9/22);  new base T (22/0);  total (31/22)
Fisher's exact test for biased strand distribution p-value = 5.88e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTTATTGAGATTGTCGCATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTACTG‑TTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTT  >  NC_000913/1604092‑1604385                                                                                                                                                  |                                                                                                                                                        gTTATTGAGATTGTCGCATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTg                                                                                                                                                   <  2:260211/151‑1 (MQ=255)       gagaTTGTCGCATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTG‑TTTGGtt                                                                                                                                                >  1:147858/1‑148 (MQ=255)         gaTTGTCGCATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTTGTTTGAcc                                                                                                                                           >  1:694872/1‑151 (MQ=255)           ttGTCGCATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTG‑TTTTGGTCGAcc                                                                                                                                           >  1:372773/1‑149 (MQ=255)               cGCATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTTGACCCTCGGc                                                                                                                                     >  1:805590/1‑151 (MQ=255)               cGCATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGc                                                                                                                                     >  2:138484/1‑151 (MQ=255)                 cATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGGTCGATATTTTG‑TTTGGTTCGCCCACCGGcc                                                                                                                                    >  2:804450/1‑150 (MQ=255)                 cATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCct                                                                                                                                   <  2:147817/151‑1 (MQ=255)                  aTTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGGGCGGTATTTTG‑TTTTGTTCGGCCATCGGCctc                                                                                                                                  >  2:358320/1‑151 (MQ=255)                      ggTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTgcg                                                                                                                              <  2:530351/151‑1 (MQ=255)                      ggTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTgcg                                                                                                                              <  1:72824/151‑1 (MQ=255)                      ggTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTgc                                                                                                                               <  1:159206/150‑1 (MQ=255)                          cAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGGTATTTTG‑TTTTGTTTGACCAACGGCCTCTGCGcc                                                                                                                            >  1:126608/1‑149 (MQ=255)                          cAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGGTATTTTG‑TTTTGTTCGACCATCGGCCTCTGCGcc                                                                                                                            >  1:697016/1‑149 (MQ=255)                              tAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCc‑attgc                                                                                                                      <  1:807634/150‑1 (MQ=255)                                  ccGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTgg                                                                                                                 <  1:1025968/151‑1 (MQ=255)                                   cgcgAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTG‑TTTTGGTCGACCATCGGCCCCTGCGCC‑CTTGCATTggg                                                                                                                >  1:749885/1‑151 (MQ=255)                                   cgcgAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTTGACCATCGGCCTCTTCGCC‑CTTTCATTtgg                                                                                                                >  1:1031040/1‑151 (MQ=255)                                       aaTGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTa                                                                                                            <  2:133104/151‑1 (MQ=255)                                        aTGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTT‑TTTGGTTTGACCCTCGGCCTCTGCGCC‑CTTTCATTtgggg                                                                                                              >  1:636739/1‑146 (MQ=255)                                        aTGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTAc                                                                                                           <  1:199322/151‑1 (MQ=255)                                           ttAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGAGTGTTATTTTGTTTTGGTTCG‑CCATCGGGCTCCGGGCC‑ATTTGATTGGGGGTatt                                                                                                          >  1:242594/1‑147 (MQ=255)                                            tAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGGTCGATATTTTT‑TTTGGTTTGACCATCGGCCTCTGCGCC‑CTTGCATTGGGGGGACTG‑tt                                                                                                      >  2:629847/1‑151 (MQ=255)                                            tAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGGTCGATATTTTT‑TTTGGTTCGACCATCGGCCCCTGCGCC‑CTTTCATTGGGGGGACTG‑tt                                                                                                      >  1:770177/1‑151 (MQ=255)                                            tAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTACTG‑t                                                                                                       <  2:933947/150‑1 (MQ=255)                                                   cAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTACTG‑TTTCaaa                                                                                                 <  2:232203/149‑1 (MQ=255)                                                   cAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTACTG‑TTTCaa                                                                                                  <  2:698620/148‑1 (MQ=255)                                                      tatGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTG‑TTTTGTTTGACCATCGGCCTCTGCGCC‑CTTTCCTTGGGGGGACTG‑TTTCAAAgtgg                                                                                             >  1:381758/1‑150 (MQ=255)                                                               gTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTACTG‑TTTCAAAGTGGTGTGCCGAt                                                                                    <  2:802922/150‑1 (MQ=255)                                                                   aGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGGTCGATATTTTT‑TTTTGTTTGGCCAACGGCCCCTGCGCC‑ATTGCCTTGGGGGGAATG‑TTTTAAAGTGGGGGGGCGGTGCCg                                                                                >  1:646150/1‑150 (MQ=255)                                                                     cACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGAACGATATTTTG‑TTTGGTTTGACCATCCGCCTCTGCGCC‑CATGCCTTTGGGGGTCTG‑TTTTCAAGGGGGGTGGCGATGCCGCt                                                                              >  1:547666/1‑150 (MQ=255)                                                                       ccAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTACTG‑TTTCAAAGTGGTGTGCCGATGCCGCTGGc                                                                           <  2:820557/151‑1 (MQ=255)                                                                       ccAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGAGTGATATTTTG‑TTTTGTTTGACCATCGGCCTCCCCGCC‑CTTGCCTTTGGCGGACTG‑TTTTTAAGTGGTGTGCCGGCGCCGCCgg                                                                            >  2:643853/1‑150 (MQ=255)                                                                          gTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTG‑TTTTGGTCGACCATCGGGCTCTGCGCC‑CTTTCATTGGGGGTACTG‑TTTTCAACAGGGGGGCCGACGCCGCAgg                                                                            >  1:1017812/1‑147 (MQ=255)                                                                                      gcattggcattgTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGGTCGGTATTTTT‑TTTGGTTCGCCCCTCGGCCCCTCCGCC‑ATTGCATTGGGCGGACTG‑TTTTAAAATGGGGTGCCGCTGCCGCTGGCGGTACTCCTGACCtt                                                            >  1:610335/1‑151 (MQ=255)                                                                                       cattggcattgTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTACTG‑TTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTa                                                           <  1:809011/151‑1 (MQ=255)                                                                                           ggcattgTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGAGCGAAAATTTG‑TTTGGGTCCACCAAGCGCCCCTCGGCCTTTTCCATTGGG‑GTAAAG‑TTTCATAGAGGGGGGCCCAGGCCGCCGGCGGGACTCCTCACCTTatt                                                         >  1:134010/1‑147 (MQ=255)                                                                                            gcattgTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTG‑TTTTGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTTGGCGGACTG‑TTTTTAAGGGGGGTGCCGATGCCGCTGGCGATAATCCTGACCtt                                                            >  1:150844/1‑145 (MQ=255)                                                                                             cattgTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTACTG‑TTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTc                                                     <  2:506844/151‑1 (MQ=255)                                                                                                tgTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTG‑TTTTGGTCGGCCAACCGCCTCTGCGCC‑CTTTCATTGGGGGTACTG‑TTTTAAAGGGGGGTGCCGAGGCCGCTGGCGGTACTCCTGACCTTTCTGCTc                                                     >  2:282016/1‑148 (MQ=255)                                                                                                           cGCTAACGATGGTGATTGTCAGTGGCGGGATTGATATTTTG‑TTTGGTTTGCCCATCCGCCTCTGCTCC‑CTTGTATTTGGCGTACTGTTTTCAAAG‑GGTGTGCCGCTGCCGCCGGCGGTACTTCTGACCTTCCTGCTCGGCGCGATGTGCg                                        >  2:26074/1‑150 (MQ=255)                                                                                                           cGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTG‑TTTTGTTTGACCATCGGCCTCTGCGCC‑CTTGCCTTGGGGGGACTG‑TTTTTAAAAGGGGTGGCGGTGCCCCTGGCGAGACTCCCGACCTTACTGCTCGGCGCCTTGTGCgg                                       >  2:528643/1‑151 (MQ=255)                                                                                                            gCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTACTG‑TTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCggg                                      <  2:215650/151‑1 (MQ=255)                                                                                                                         aTTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTACTG‑TTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCg                         <  1:362319/151‑1 (MQ=255)                                                                                                                                  ggCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTACTG‑TTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGattaatta                <  1:566932/151‑1 (MQ=255)                                                                                                                                  ggCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTACTG‑TTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGattaatta                <  2:61560/151‑1 (MQ=255)                                                                                                                                  ggCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTACTG‑TTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGattaatt                 >  2:1042258/1‑150 (MQ=255)                                                                                                                                         tCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTACTG‑TTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATAc         >  1:360940/1‑151 (MQ=255)                                                                                                                                            atatTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTACTG‑TTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCaa      <  2:749683/151‑1 (MQ=255)                                                                                                                                              atTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTACTG‑TTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCaa      >  2:363376/1‑149 (MQ=255)                                                                                                                                              atTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTACTG‑TTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCaa      >  2:339884/1‑149 (MQ=255)                                                                                                                                                ttCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTACTG‑TTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGt   <  2:319918/150‑1 (MQ=255)                                                                                                                                                ttCG‑TTTGGGTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTACTG‑TTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGtt  >  2:592569/1‑151 (MQ=255)                                                                                                                                                  |                                                                                                                                                        GTTATTGAGATTGTCGCATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCG‑TTTGGTTCGACCATCGGCCTCTGCGCC‑ATTGCATTGGGCGTACTG‑TTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTT  >  NC_000913/1604092‑1604385

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑