Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,574,051	0	G	T	40.7%	93.3 / 22.1	54	V384V (GTC→GTA)	pqqL	putative periplasmic M16 family zinc metalloendopeptidase
Reads supporting (aligned to +/- strand):  ref base G (7/25);  new base T (21/1);  total (28/26)
Fisher's exact test for biased strand distribution p-value = 4.23e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGACGTTTCGAAAGTTGATATGTCTCTTCCGGCGACAAGAACGGCGTATTATTTAATGAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCAACTCTGCCA‑TTAATGCATTCGCAGCATCCTGCATATTATCGTCTCG‑TGCATTTACACGGAAAAACAGCGACTGATAATCGGGTGCAATTTTAACGCTGC  >  NC_000913/1573902‑1574199                                                                                                                                                      |                                                                                                                                                         aGACGTTTCGAAAGTTGATATGTCTCTTCCGGCGACAAGAACGGCGTATTATTTAATGAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGa                                                                                                                                                         <  1:208127/151‑1 (MQ=255)                    atGTCTCTTCCGGCGACAAGAACGGCGTATTATTTAATGAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCATCCAGGTGAGGCGGGTAGATTTTACATCATCGAGT‑TCTTcagc                                                                                                                                     <  2:931181/151‑1 (MQ=255)                          ctTCCGGCGACAAGAACGGCGTATTATTTAATGAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGa                                                                                                                                  <  1:5471/148‑1 (MQ=255)                                  gACAAGAACGGCGTATTATTTAATGAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCt                                                                                                                       <  1:141432/151‑1 (MQ=255)                                  gACAAGAACGGCGTATTATTTAATGAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGGAGATTTTAAATCATCGAGT‑TTTTCAACAGAAAAAACaaac                                                                                                                        >  1:1519/1‑147 (MQ=255)                                   aCAAGAACGGCGTATTATTTAATGAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTTACATCATCGAGT‑TTTTCAGCAGAAAAAACATGCt                                                                                                                       >  1:272716/1‑150 (MQ=255)                                   aCAAGAACGGCGTATTATTTAATGAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTg                                                                                                                      <  2:675647/151‑1 (MQ=255)                                   aCAAGAACGGCGTATTATTTAATGAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTg                                                                                                                      <  1:384684/151‑1 (MQ=255)                                    cAAGAACGGCGTATTATTTAATGAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTTACATCATCGAGG‑TCTTTCGCAGAAAAAACATGc                                                                                                                        >  1:141269/1‑148 (MQ=255)                                      aGAACGGCGTATTATTTAATGAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATc                                                                                                                   <  1:217433/151‑1 (MQ=255)                                        aaCGGCGTATTATTTAATGAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGATAGAATTGGCATCATTCGGT‑TATTACGCCGGAAAACCAAGCt                                                                                                                       >  1:506926/1‑145 (MQ=255)                                            gCGTATTATTTAATGAGCTGGATGCCAGGCGACTCGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGt                                                                                                            <  2:181091/151‑1 (MQ=255)                                               tattatTTAATGAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCCAGG‑TCTTCCGCAGAAAAAACATGCTGATCaa                                                                                                                 >  1:33967/1‑144 (MQ=255)                                                attattTAATGAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGcc                                                                                                        <  1:753610/151‑1 (MQ=255)                                                  tattTAATGAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCa                                                                                                       <  1:752571/150‑1 (MQ=255)                                                  tattTAATGAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCa                                                                                                       <  2:653389/150‑1 (MQ=255)                                                       aaTGAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCAActct                                                                                                  <  1:907901/150‑1 (MQ=255)                                                       aaTGAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCAActct                                                                                                  <  1:573625/150‑1 (MQ=255)                                                       aaTGAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGGAGATTTTACATCATCGAGG‑TTTTTAGCAGAAAAAACAAGCTGATCAA‑TGGGTGGCAAatc                                                                                                   >  1:475328/1‑149 (MQ=255)                                                          gAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCAACTCTGCCa                                                                                              <  1:933958/151‑1 (MQ=255)                                                              tGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTTACATCATCGAGT‑TCTTCAGCAGAAAAAACATGCTGTTCAA‑TGGTTGTCCACTCTGCCC‑tt                                                                                           >  2:499306/1‑149 (MQ=255)                                                                 aTGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTTACATAATCCAGG‑TCTTCAGCAGAAAAACACAGCTGATAAA‑TGGGTGCCCACTCTGCCA‑TTAAt                                                                                        >  2:654619/1‑149 (MQ=255)                                                                 aTGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCAACTCTGCCA‑TTAATGc                                                                                      <  2:16981/151‑1 (MQ=255)                                                                  tGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTTAACTCATCCAGT‑TTTTTCGCAGAAAAAACAAGCCTATCCA‑AGGTTTCCAACTCCGCCA‑tt                                                                                           >  2:74890/1‑145 (MQ=255)                                                                   gCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCAACTCTGCCA‑TTAATGCAt                                                                                    <  1:835566/151‑1 (MQ=255)                                                                        gCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCAACTCTGCCA‑TTAATGCATTCgca                                                                               <  1:630068/151‑1 (MQ=255)                                                                            cTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGAGAGAATTGACCACATCGAGTGTTTTTAAC‑GAAAAAACATGGTGATCAA‑TTGTTGCCAACTCTGCCA‑ATAATACATTTgca                                                                               >  2:318745/1‑147 (MQ=255)                                                                              ggTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTTACATAATCGAGT‑TCTTCTGCAGAAAAAACATGCTGATCAA‑TGGTTGCCCACTCTGCCA‑TTAATACATTCTCCGCATcc                                                                         >  2:840355/1‑151 (MQ=255)                                                                              ggTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGAATTTACATCATCGAGT‑TTTTTAGCAGAAAAAACAAGCTGATCAA‑TGGTTGCCAACTCTTCCC‑TTAATTCATTCGCAGCATcc                                                                         >  1:452955/1‑151 (MQ=255)                                                                                  aGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGAATTTTGATGAACTAGT‑TATTCAGCATACAAAACAAATTTGTTAA‑AGTTTGCCAACTATTCCA‑TTGATGCAttgggatgcgcctg                                                                       >  2:411742/1‑137 (MQ=255)                                                                                    cATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTTACACCATAGAGG‑TCTTCCGCCGAAAAACCACACTGATCAA‑TGGTTTTCAACTCTGCCC‑TTAATGCATTCGCAGCATCCTGc                                                                      >  1:393346/1‑148 (MQ=255)                                                                                      tACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTTACATCATCGAGT‑TTTTTAGCAGAAAAAACAAGCTGATTAA‑TGGTTTCCAACTCTGCCA‑TTAATTCATTCGCAGCATCCTGCAtatt                                                                 >  1:360678/1‑151 (MQ=255)                                                                                        cGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGAATTTACATCATCGAGT‑TTTTTCGCAGAAAAAACAAGCTGGTTAA‑TGGTTGCCAACTCTTCCC‑TTAATGCATTTGCAGCATCCTGCAtatt                                                                 >  1:4249/1‑149 (MQ=255)                                                                                           aaaTCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTTACATCATCCAGT‑TTTTTAGCAGAAAAAACAAGCTGATTAA‑TTGGTTCCCACTCTGCCC‑TTTATTCATTCGCAGCATCCTGCAtatt                                                                 >  1:206340/1‑146 (MQ=255)                                                                                                       gCTTGCTGATCAACCGCATTTTTCAGCCAGGGGAGGCGGGGAGATTTTTCAGCAAAGAGG‑TTTTTAGTAGAAAAAAAACAGTGAACAA‑TGGTTGCCAACTCTTTCC‑TTTATGTATTTCCCGGATCCCGCAAATTATTGTGTCGTTGCAtt                                                 >  2:164119/1‑150 (MQ=255)                                                                                                          tGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGCGT‑TTTTTTGCAGGAAAAACAAGCTGATCAA‑TGGGTGCCACCTCTTTCA‑TTAATACATTCGCAACATACTGCATAATATTATCTCG‑CGCAttt                                                >  2:267421/1‑147 (MQ=255)                                                                                                          tGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCAACTCTGCCA‑TTAATGCATTCGCAGCATCCTGCATATTATCGTCTCG‑TGCATTTaca                                             <  1:706726/150‑1 (MQ=255)                                                                                                             tGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTTACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGGTTCCAACTCTTCCA‑TTAATTCATTCGCAGCATCCTGCATATTATCGTCTCG‑TGCATTTTCACgg                                          >  1:801219/1‑150 (MQ=255)                                                                                                                tCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGAATTTACATCATCGAGG‑TCTTCAGCAGAAAAAACAAGCTGATCAA‑TGGTTGCCAACTCTGCCA‑TTAATGCATTTGCAGCATCCTGCATATTATCGTCTCG‑TGCCTTTACACGGaaa                                       >  1:744817/1‑150 (MQ=255)                                                                                                                   aCCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCAACTCTGCCA‑TTAATGCATTCGCAGCATCCTGCATATTATCGTCTCG‑TGCATTTACACGGAAAAACa                                   <  1:444109/151‑1 (MQ=255)                                                                                                                    ccGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTTACTTCATCGAGT‑TCTTCAGCAGAAAAAACATGCTGATCTA‑TGGTTTCCAACTCTTCCC‑TTAATTCATTTGCAGCATCCTGCATATTATCGTTTCC‑TGCATTTATACGGAAAAACa                                   >  1:184602/1‑150 (MQ=255)                                                                                                                      gCATTTTTCAGCCAGGTGAGGCGGGTGGATTTTTAATCATCGAGT‑TTTTTACCAGAAAAAACATGCTGGTCAA‑TGGGTGGCAACTCTTCCACTTAAT‑CATTTGCACCATCCCGCATATTATTGTCTCT‑GGCGTTTTTACGGaaaaaaa                                   >  2:903711/1‑146 (MQ=255)                                                                                                                       cATTTTTCAGCCAGGTGAGGCGGGCAGAATTTTCATCAACGCGT‑TTTTCAGCAGAAAAAACAAGTTCGTAAACTGGTTTCC‑ACTCTGCCA‑CTTATTCATTCCAAGACTCCTCCCTATTTTCGTGTCG‑TGGATTTAAACCGGAAAACa                                   >  1:861158/1‑147 (MQ=255)                                                                                                                        aTTTTTCAGCCAGGTGAGGCGGGTAGATTTTACATCATCGAGG‑TCTTCAGCAGAAAAAACACGCTGATCAA‑AGGTTGCCAACTCTGCCC‑TTAATTCATTCGCAGCATCCCGCATATTATCGTCTCG‑CGCATTTAAACGGaaaaaaaacg                                >  1:779725/1‑144 (MQ=255)                                                                                                                          ttttCAGCCAGGTGAGGCGGGTAGAGTTGTCATCATCGAGT‑TCTTCCACAGAAAAACCATGCTGATCAA‑TGGTTGCCAACTCTGCCA‑TTAATGCATTCGCAGCATCCTGCATATTATCGTCTCG‑TGCATTTATACGGAAAAACAGCGACTg                            >  2:341798/1‑151 (MQ=255)                                                                                                                            ttCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCAACTCTGCCA‑TTAATGCATTCGCAGCATCCTGCATATTATCGTCTCG‑TGCATTTACACGGAAAAACAGCGACTg                            <  1:899835/149‑1 (MQ=255)                                                                                                                                gCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCAACTCTGCCA‑TTAATGCATTCGCAGCATCCTGCATATTATCGTCTCG‑TGCATTTACACGGAAAAACAGCGACTGATAATc                      <  1:149233/151‑1 (MQ=255)                                                                                                                                     gTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCAACTCTGCCA‑TTAATGCATTCGCAGCATCCTGCATATTATCGTCTCG‑TGCATTTACACGGAAAAACAGCGACTGATAATCGGGTg                 <  1:391290/151‑1 (MQ=255)                                                                                                                                            gggTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCAACTCTGCCA‑TTAATGCATTCGCAGCATCCTGCATATTATCGTCTCG‑TGCATTTACACGGAAAAACAGCGACTGATAATCGGGTGCAAtttt          <  2:313757/151‑1 (MQ=255)                                                                                                                                                 gATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCAACTCTGCCA‑TTAATGCATTCGCAGCATCCTGCATATTATCGTCTCG‑TGCATTTACACGGAAAAACAGCGACTGATAATCGGGTGCAATTTTAACGc     >  1:27437/1‑151 (MQ=255)                                                                                                                                                  aTTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCAACTCTGCCA‑TTAATGCATTCGCAGCATCCTGCATATTATCGTCTCG‑TGCATTTACACGGAAAAACAGCGACTGATAATCGGGTGCAATTTTAACGCt    <  1:292221/151‑1 (MQ=255)                                                                                                                                                  aTTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCAACTCTGCCA‑TTAATGCATTCGCAGCATCCTGCATATTATCGTCTCG‑TGCATTTACACGGAAAAACAGCGACTGATAATCGGGTGCAATTTTAACGCt    >  2:946484/1‑151 (MQ=255)                                                                                                                                                    ttGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCAACTCTGCCA‑TTAATGCATTCGCAGCATCCTGCATATTATCGTCTCG‑TGCATTTACACGGAAAAACAGCGACTGATAATCGGGTGCAATTTTAACGCTg   <  1:146766/150‑1 (MQ=255)                                                                                                                                                     tGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCAACTCTGCCA‑TTAATGCATTCGCAGCATCCTGCATATTATCGTCTCG‑TGCATTTACACGGAAAAACAGCGACTGATAATCGGGTGCAATTTTAACGCTgc  <  1:819198/150‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                         AGACGTTTCGAAAGTTGATATGTCTCTTCCGGCGACAAGAACGGCGTATTATTTAATGAGCTGGATGCCAGGCGACTGGTCAGCATACGTAAATCACGTTCAGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGT‑TCTTCAGCAGAAAAACCATGCTGATCAA‑TGGTTGCCAACTCTGCCA‑TTAATGCATTCGCAGCATCCTGCATATTATCGTCTCG‑TGCATTTACACGGAAAAACAGCGACTGATAATCGGGTGCAATTTTAACGCTGC  >  NC_000913/1573902‑1574199

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑