Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,105,489	0	C	A	43.4%	83.2 / 26.7	54	Q353K (CAA→AAA)	mltC	membrane‑bound lytic murein transglycosylase C
Reads supporting (aligned to +/- strand):  ref base C (25/5);  new base A (0/23);  total (25/29)
Fisher's exact test for biased strand distribution p-value = 2.61e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGGCAGCGTGCTGCGAGTCTTTTCGAATGATAAGATTCAGGCTGCCAATATTATTAACACCATGACGCCGGGCGATGTTTATCAGACGCTGACGACCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTATTTGCCACAGGTAACAAAAAACCAGTCCGCGAAGTTGAT  >  NC_000913/3105341‑3105639                                                                                                                                                     |                                                                                                                                                       aggcagCGTGCTGCGAGTCTTTTCGAATGATAAGATTCAGGCTGCCAATATTATTAACACCATGACGCCGGGCGATGTTTATCAGACGCTGACGACCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCaa                                                                                                                                                      <  2:328879/151‑1 (MQ=255)     agCGTGCTGCGAGTCTTTTCGAATGATAAGATTCAGGCTGCCAATATTATTAACACCATGACGCCGGGCGATGTTTATCAGACGCTGACGACCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAAt                                                                                                                                                  >  1:595257/1‑151 (MQ=255)             gcGAGTCTTTTCGAATGATAAGATTCAGGCTGCCAATATTATTAACACCATGACGCCGGGCGATGTTTATCAGACGCTGACGACCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTAcc                                                                                                                                            <  2:642787/149‑1 (MQ=255)                 gTCTTTTCGAATGATAAGATTCAGGCTGCCAATATTATTAACACCATGACGCCGGGCGATGTTTATCAGACGCTGACGACCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTAccgccgcc                                                                                                                                      >  2:421555/1‑151 (MQ=255)                 gTCTTTTCGAATGATAAGATTCAGGCTGCCAATATTATAAACACCATGACGCCGGGCGATGTTTACCAGACGCTGACGACCCGCCATCCCTCTGCGGAATCCCGCCGTTATCTTTATAAAGTGAATACCGCGAAAAAATCCTAccgccg                                                                                                                                        <  1:723195/149‑1 (MQ=255)                       tCGAATGATAAGATTCAGGCTGCCAATATTATTAACACCATGACGCCGGGCGATGTTTATCAGACGCTGACGCCCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATaa                                                                                                                                 <  2:709788/150‑1 (MQ=255)                         gAATGATAAGATTCAGGCTGCCAATATTATTAACACCATGACGCCGGGCGATGTTTATCAGACGCTGACGACCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTc                                                                                                                              >  1:970449/1‑151 (MQ=255)                          aaTGATAAGATTCAGGCTGCCAATATTATTACCCCCATGACGCCGGGAGATGTTTATCAGAGGCTGACGACCCGCCATCCCTCTGCGGAACCTCGCCGTTATCTTTATAAAGTGAATGCCGCTTAAAAATCCTACCGCCGCCGATAATTc                                                                                                                              <  1:748603/150‑1 (MQ=255)                               tAAGATTCAGGCTGCCAATATTATTAACACCATGACGCCGGGCGATGTTTATCAGACGCTGACGACCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTa                                                                                                                         >  2:536289/1‑150 (MQ=255)                                aaGATTCAGGCTGCCAATATTATTAACACCATGACGCCGGGCGATGTTTATCAGACGCTGACGACCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTaa                                                                                                                        <  2:659748/150‑1 (MQ=255)                                 aGATTCAGGCTGCCAATATTATTAACACCATGACGCCGGGCGATGTTTATCAGACGCTGACGACCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAAcc                                                                                                                      <  2:638665/151‑1 (MQ=255)                                        ggatGCCAATATTATTACCCCCATGACGCCGGGGGATGTTTATCATACTCGGAGGACCCGCCTTCCCGCTGCGAAATCTCGCCGTTTTCTTTATAAAGGGAATCCCCCGAAAAAATCCTCCCGCCGCCAATAATTCCATTAACCGcccc                                                                                                                 <  1:606223/146‑1 (MQ=255)                                         gCTGCCAATATTATTAACACCATGACGCCGGGCGATGTTTATCAGACGCTGACGACCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTg                                                                                                               >  2:666673/1‑150 (MQ=255)                                                     attaACACCATGACGCCGGGCGATGTTTATCAGACGCTGACGACCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAggg                                                                                                  >  1:551185/1‑151 (MQ=255)                                                       taACACCATGACGCCGGGCGATGTTTATCAGACGCTGACGACCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGc                                                                                                >  1:960760/1‑151 (MQ=255)                                                        acccccAGGACGCCGGGCGATGTTTATCAGCCGCTGACGCCCCGCCATCCCTCGGCGAAATCTCGCCTTTATCTTTATAAAGTGAATCCCGCGAAAAAACCCTCCCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAgggg                                                                                                 <  2:996705/145‑1 (MQ=255)                                                        aaCCCCATGCCGCGGGGCGTTTTTTATAAGCCGCTGACGCCCCGCCATCCCTCTGGGGAATCTCGCCGTTATCTTTATAAAGTGAATCCCGCGAAAAAACCCTCCCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAgg                                                                                                   <  2:526528/147‑1 (MQ=255)                                                        aaCACCATGACGCCGGGCGATGTTTATCAGACGCTGACGACCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGc                                                                                                >  1:952109/1‑150 (MQ=255)                                                         acacCATGACGCCGGGCGATGTTTATCAGACGCTGACGACCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCa                                                                                               >  2:392932/1‑150 (MQ=255)                                                             cATGACGCGGGGCGTTTTTTATCAGCGGGTGCGGCCCCCCCACCCCTCGGCGAAAGCTCCCCGTTATTTTTATAAAGTAAATCCCGCGAAAAAACCCTCCCCCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCaaa                                                                                             <  1:473179/148‑1 (MQ=255)                                                                  cGCCGGGCGATGTTTATCAGACGCTGACGACCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTAt                                                                                     >  2:996646/1‑151 (MQ=255)                                                                      gggCGATGTTTATCAGACGCTGACGACCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCcac                                                                                 >  2:811325/1‑151 (MQ=255)                                                                      gggCGATGTTTATCAGACGCTGACGACCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCcac                                                                                 >  1:235934/1‑151 (MQ=255)                                                                           aTGTTTATCAGACGCTGACGACCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATcac                                                                            >  2:960512/1‑151 (MQ=255)                                                                            tttttATCAGCCGCTGACGACCCGCCATCCCTCGGCGAAATCCCGCCTTTATTTTTAAAAAGTAAATCCCGCGAAAAAATCCTCCCCCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATc                                                                              <  2:39708/146‑1 (MQ=255)                                                                                 accagccccTGACGCCCCCCCACCCCTCGGGGAAATCTCCCCGTTATCTTAAAAAAGTAAATCCCGCAAAAAAACCCTCCCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAAtt                                                                        <  2:866859/141‑1 (MQ=255)                                                                                   cAGACGCTGACGACCCGCCTCCCCTCGGCGGATTCCCCCCGTTTTCTTTAAAAAGAAAAAACCCCGAAAAAACCCCCCCGCGGCCAATAATTCCATAACCCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAAtt                                                                        <  1:440950/147‑1 (MQ=255)                                                                                   cAGACGCTGACGACCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGt                                                                    >  2:807333/1‑151 (MQ=255)                                                                                              gacCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTg                                                         >  2:640478/1‑151 (MQ=255)                                                                                               acCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTgg                                                        >  2:534470/1‑151 (MQ=255)                                                                                                cccccctccccTCTGCGAAATCTCGCGTTTTTTTTTAAAAAGTAAACCCCCCAAAAAAACCCTCCCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGc                                                               <  1:867960/135‑1 (MQ=255)                                                                                                ccccccACCCCTCTGCGAAATCTCGCCGTTATTTTTAAAAAGTAAATCCCGCGAAAAAACCCTCCCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAAtt                                                          <  2:596711/148‑1 (MQ=255)                                                                                                cccGCCTCCCCCCTGGGGAATCTCGCCTTTGTCTTTAAAAAGTGAATCCCGCAAAAAAACCCTCCCGCCGCGGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTggg                                                       <  2:352873/151‑1 (MQ=255)                                                                                                  cgcatacccgcgccGGAATCTCGCATTTATCTTTATAGAGTAAATACCCCGAAAAATCCCTCCCGCCGCCAATATTTCCATAAACCGCCCCTGACGAGGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTg                                                         <  1:64899/134‑1 (MQ=255)                                                                                                            ctGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAat                                           >  2:723034/1‑151 (MQ=255)                                                                                                              gCGGAATCCCGCGTTTATTTTTAAAAGGTAAACCCCGCGAAAAACCCCTCCCCCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCa                                             <  1:402877/147‑1 (MQ=255)                                                                                                                     ctcCCCGTTATTTTTAAAAAGTAAATCCCGCGAAAAAACCCTCCCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTAttt                                      <  2:612993/147‑1 (MQ=255)                                                                                                                     cccGCCTTTTTCTTTAAAAAGTAAATCCCGCAAAAAACCCCTCCCCCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTATTTGc                                    <  1:329039/147‑1 (MQ=255)                                                                                                                          gtttcgttttATAAGGTAAAACCCGCGAAAAAATCCAGCTGCCGCCAATATTTCCATTGACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTATTTGCcaca                                <  2:86922/141‑1 (MQ=255)                                                                                                                          cGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTATTTGCCACAg                               >  2:42493/1‑149 (MQ=255)                                                                                                                            ttATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTATTTGCCACAGGTa                            >  1:582335/1‑150 (MQ=255)                                                                                                                            taatttttAAAAAGGGAATCCCGCAAAAAACTCCTCCCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTATTTGCCACAGGTa                            <  1:450750/145‑1 (MQ=255)                                                                                                                               tCTTTAAAAAGTAATTCCCGCAAAAAAATCCTACCGCCGCCGAAAATCCCTTTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTATTTGCCACAGGTAACa                         <  2:1021863/150‑1 (MQ=255)                                                                                                                                 tttAAAAAGTGAATCCCGCGAAAAAACCCTCCCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTATTTGCCACAGGTaa                           <  2:806884/146‑1 (MQ=255)                                                                                                                                 tttAAAAAGTGAATCCCGCAAAAAAACCCTCCCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTATTTGCCACAGGTAACa                         <  2:931037/148‑1 (MQ=255)                                                                                                                                  ttATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTATTTGCCACAGGTAACaaaa                      >  1:772853/1‑150 (MQ=255)                                                                                                                                    ataAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTATTTGCCACAGGTAACAAAAAAc                   >  1:318382/1‑151 (MQ=255)                                                                                                                                      aagtgaaaccccGCGAAAAAACCCTCCCGCCGCCAATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTATTTGCCACAGGTAACAAAAAACCa                 <  2:546214/141‑1 (MQ=255)                                                                                                                                      aaaGGGAAACCCACGAAAAAACCCGCCCGCATCGGAAAATACCATTAGCCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAAGTTCATTTTGCAAATTGGGAATGTTTGCAATTATTTGCCACAGGTAACAAAAAACCa                 <  1:88595/151‑1 (MQ=255)                                                                                                                                        aGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTATTTGCCACAGGTAACAAAAAACCAGt               >  2:36673/1‑151 (MQ=255)                                                                                                                                           gAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTATTTGCCACAGGTAACAAAAAACCAGTCcg            >  2:994449/1‑151 (MQ=255)                                                                                                                                            aaTCCCGCGAAAAATTCCTCCCCCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTATTTGCCACAGGTAACAAAAAACCAGTCcg            <  1:665365/150‑1 (MQ=255)                                                                                                                                            aaTACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTATTTGCCACAGGTAACAAAAAACCAGTCcgc           >  2:185973/1‑151 (MQ=255)                                                                                                                                               aCCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTATTTGCCACAGGTAACAAAAAACCAGTCCGCGa         >  2:854931/1‑150 (MQ=255)                                                                                                                                                    gcAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTATTTGCCACAGGTAACAAAAAACCAGTCCGCGAAGTTg    >  2:191164/1‑150 (MQ=255)                                                                                                                                                     cAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTATTTGCCACAGGTAACAAAAAACCAGTCCGCGAAGTTGAt  >  2:743128/1‑151 (MQ=255)                                                                                                                                                     |                                                                                                                                                       AGGCAGCGTGCTGCGAGTCTTTTCGAATGATAAGATTCAGGCTGCCAATATTATTAACACCATGACGCCGGGCGATGTTTATCAGACGCTGACGACCCGCCATCCCTCTGCGGAATCTCGCCGTTATCTTTATAAAGTGAATACCGCGCAAAAATCCTACCGCCGCCGATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGAATGTTTGCAATTATTTGCCACAGGTAACAAAAAACCAGTCCGCGAAGTTGAT  >  NC_000913/3105341‑3105639

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: ‑