Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,701,310	0	A	C	41.7%	71.2 / 13.1	48	T118T (ACA→ACC)	malY	PLP‑dependent beta‑cystathionase and maltose regulon regulator
Reads supporting (aligned to +/- strand):  ref base A (23/5);  new base C (0/20);  total (23/25)
Fisher's exact test for biased strand distribution p-value = 3.28e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTTTCTCGCGGCTATTGCCCACTGGTTTTCCACCCAGCATTACACCGCCATCGATTCTCAGACGGTGGTGTATGGCCCTTCTGTCATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGATATGGGCAAGTTGGAAGCCGTGTTGGCGAAACCAGAATGTAAAATTATG  >  NC_000913/1701160‑1701454                                                                                                                                                        |                                                                                                                                                 gTTTCTCGCGGCTATTGCCCACTGGTTTTCCACCCAGCATTACACCGCCATCGATTCTCAGACGGTGGTGTATGGCCCTTCTGTCATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCcacaca                                                                                                                                                  <  1:201561/151‑1 (MQ=255)    tctcGCGGCTATTGCCCACTGGTTTTCCACCCAGCATTACACCGCCATCGATTCTCAGACGGTGGTGTATGGCCCTTCTGTCATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCacacac                                                                                                                                                 <  2:983759/149‑1 (MQ=255)              aTTGCCCACTGGTTTTCCACCCAGCATTACACCGCCATCGATTCTCAGACGGTGGTGTATGGCCCTTCTGTCATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACg                                                                                                                                     >  1:815010/1‑151 (MQ=255)                      ttgttttcCCACCCCGAATTCCCCCGCAATCGATTCTCAGCCGGTGGTTTTTGTCCCTTGTATCATCTATATGGTTGCAAACCTGCTCCTTCAGTGTATTGAAC‑CGGTTGAAGGCGTGGTGTCACACCCCCCCGCCTATGACGCATTTTa                                                                                                                              <  2:389891/146‑1 (MQ=255)                        ggTTTTCCACCCAGCATTACACCGCCATCGATTCTCAGACGGTGGTGTATGGCCCTTCTGTCATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACa                                                                                                                            >  1:872608/1‑150 (MQ=255)                        ggTTTTCCACCCAGCATTACACCGCCATCGATTCTCAGACGGTGGTGTATGGCCCTTCTGTCATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACa                                                                                                                            >  2:103380/1‑150 (MQ=255)                          ttttCCCCCCAGCATTCCCCCGCCATCGATTCTCAGAGGGTGTGGTAGGGCCCTTCTGTCATATAAATGGTTCCAGAATTGCTTCGTCAGTGGTCAGAAC‑AAGGTGAGGGCGTGGTGTTCCACACACCCGCCTATGACGCATTTTACAAg                                                                                                                          <  1:1047053/150‑1 (MQ=255)                               cccccAGCATTACCCCGCCATCGATTCTCAGACGGTGGTGTATGGCCCTTCTGTCATCTATATGGTTTCAGAACTGTTTCGTCAGTGGTCTAAAA‑CAGGTGAGGGCGTGGTGATCCACACCCCCGCCTATGACGCATTTTACAAGGCCAtt                                                                                                                    <  1:21659/149‑1 (MQ=255)                                  ccAGCATTACACCGCCATCGATTCTCAGACGGTGGTGTATGGCCCTTCTGTCATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGa                                                                                                                  >  1:541916/1‑150 (MQ=255)                                    aGCATTACCCCGCCAGCGTTTCTCAGAGGTTGGTGTATGGCCCTTCTGTCATTTATGTGTTTTCAGAACTGTTTCGCCAGTGTTCTAAAA‑AGGGTGAGGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAg                                                                                                                <  2:228658/150‑1 (MQ=255)                                       aTTACCCCGCCTTCGATTCTAAGGCGGTGGTGTATGGCCCTCCTGTCATTTATATGGTTCAAGAACTTATTCGTCAGTGGTTTAAAC‑CGGGTGAAGGCGTGGTGATCCACACCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGt                                                                                                              <  2:923184/149‑1 (MQ=255)                                            acCGCCATCGATTCTCAGACGGTGGTGTATGGCCCTTCTGTCATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAgc                                                                                                       >  1:227633/1‑151 (MQ=255)                                            acCGCCATCGATTCTCAGACGGTGGTGTATGGCCCTTCTGTCATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAgc                                                                                                       >  1:161880/1‑151 (MQ=255)                                               gCCATCGATTCTCAGACGGTGGTGTATGGCCCTTCTGTCATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAgcgc                                                                                                     >  1:302195/1‑150 (MQ=255)                                                   tCGATTCTCAGAGGGTTGTGTATGCCCGTCCTTACATTTATTTGGTTTCAAACCCGATACCACAGGGGTTTAAAC‑AAAGAGGTGGCGTGGTGACCAACCCACCCGCCTATGACGCATTTTACAAGGCCATTGGAGGTAACCAGCGcaca                                                                                                  <  2:953667/149‑1 (MQ=255)                                                    cgtttCTCAGCCGGTGGTGTAGGGCCCTTCGGTCATCTATATGGTTTCAGAACTGTTTCGTCGGTGGTCTGAAA‑AAGGGGAAGGGGTGGTGATCCACACCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGt                                                                                                <  2:525240/147‑1 (MQ=255)                                                    cGATTCTCAGACGGTGGTGTATGGCCCTTCTGTCATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGt                                                                                                >  1:623999/1‑150 (MQ=255)                                                      aTTCTCAGACGGTGGTGTATGGCCCTTCTGTCATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAAt                                                                                             >  2:147390/1‑151 (MQ=255)                                                       ttCTCAGACGGTGGTGTATGGCCCTTCTGTCATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATg                                                                                            >  2:744525/1‑151 (MQ=255)                                                       ttCTCAGACGGTGGTGTATGGCCCTTCTGTCATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATg                                                                                            >  2:173299/1‑151 (MQ=255)                                                           cAGACGGTGGTGTATGGCCCTTCTGTCATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCg                                                                                        >  2:29207/1‑151 (MQ=255)                                                              aCGGTGTTGTATGGCCTTTTTGTTATCTATGTGTTTTCAGAACTGATTCTTCAGTGGTCTGAAA‑CGGTTGAGGGCGTGGTGATCCACGCCGCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGtt                                                                                      <  1:105471/150‑1 (MQ=255)                                                                    gtttATGCCCTTTCCTTCTTCTTTGTGGTTTCAGACCTGTTTCTTCTGTGGTCTGAAA‑TAGGGGACGGGGTGTTGATCCTCACCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTa                                                                                <  2:110538/147‑1 (MQ=255)                                                                        aTGGCCCTTCTGTCATTTATATGTTTCCAGAACTGATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGGGGGGTGACCCACACCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTagag                                                                             <  1:659958/149‑1 (MQ=255)                                                                          ggCCCTTCTGTCATATATAGTGTTTCATAACTGTTTCGTCAGTGTTCTAAAA‑CAGGTGAAGGCGTGGTGATCCACCCCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGc                                                                         <  2:281804/151‑1 (MQ=255)                                                                             ccTTCTGTCATCTATAGGGTTTCAGACCTGATTCGTCAGGGTTCTAAAA‑CAGGTAAAGGCGTGGTGATCCACACCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAg                                                                       <  2:1056097/150‑1 (MQ=255)                                                                                       tttataTGGTTTCAGAACGGATTGTTCAGTGTTCTGAAA‑CAGGTAAAGGCGTGTTGATCCACACCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGAtggt                                                              <  2:538404/147‑1 (MQ=255)                                                                                       tCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGAtggttg                                                            >  1:614966/1‑151 (MQ=255)                                                                                          atatGGTTTCAGAACTGATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATggttggtt                                                         >  1:616700/1‑151 (MQ=255)                                                                                             tGGTTCAAGACCTGTTTCTTAAGTGGT‑TGAAAGCAGGTGAGGGGTTGGTGACCCACCCCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCt                                                                    <  2:990615/137‑1 (MQ=255)                                                                                              gttttCAAAACTGATTCGTCGGTGGTCGAAAA‑CGGGTGAGGGGGTGGTGATCCACACCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGAtggtt                                                             <  2:32671/141‑1 (MQ=255)                                                                                                tttCAGAACTGATTCGTCAGTGGTCTGAAA‑CAGGCGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCg                                                    >  2:276923/1‑150 (MQ=255)                                                                                                    aGAACTGATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGATATg                                               >  2:310344/1‑151 (MQ=255)                                                                                                    aGAACTGATTCGTCAGTGGTATGAAA‑CAGGTGAAGGCTTGGTGATCCACACATCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGatat                                                >  2:772766/1‑150 (MQ=255)                                                                                                          gATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGATATGGGCa                                           >  2:83611/1‑149 (MQ=255)                                                                                                            ttCGTCAGTGGTCTGAAA‑CGGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGATATGGGCAAg                                         <  1:960049/149‑1 (MQ=255)                                                                                                            ttCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGATATGGGCAAGt                                        >  1:297253/1‑150 (MQ=255)                                                                                                               gTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGATATGGGCAAGTTgg                                     >  1:550473/1‑150 (MQ=255)                                                                                                                 cAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGATATGGGCAAGTTGGa                                    >  2:276449/1‑149 (MQ=255)                                                                                                                      gTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGATATGGGCAAGTTGGAAGCCgtg                             >  2:567983/1‑151 (MQ=255)                                                                                                                           aaa‑CAGGTGAGGGCGGGGTGACCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGATATGGGCAAGTTGGAAGCCGTGTCgg                         <  2:286591/150‑1 (MQ=255)                                                                                                                           aaa‑CAGGTGAAGGGGGGGTGATCCACACCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGATATGGGCAAGTTGGAAGCCGTGTTg                          <  1:984505/149‑1 (MQ=255)                                                                                                                           aaa‑CAGGGAAGGGGGTGGGGATCCACCCCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGATATGGGCAAGTTGGAAGCCgtgt                            <  1:103410/147‑1 (MQ=255)                                                                                                                            aacaaGGTGAAGGCGGGGTGACCCCCCCCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGATATGGGCAAGTTGGAAGCCGTGtt                           <  2:778334/144‑1 (MQ=255)                                                                                                                              actggTGAAGGCGTGGTTCTCCACCCCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGATATGGGCAAGTTGGAAGCCgtgt                            <  2:642214/142‑1 (MQ=255)                                                                                                                                 ggTGAAGGCGTGGTGATCCCCCCCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGATATGGGCAAGTTGGAAGCCGTGTTGGCGaaa                    <  2:72053/150‑1 (MQ=255)                                                                                                                                          gtggtgATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGATATGGGCAAGTTGGAAGCCGTGTTGGCGAAACCAGAATGt           >  2:732274/1‑150 (MQ=255)                                                                                                                                          ggggggacccccacccCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGATATGGGCAAGTTGGAAGCCGGGTTGGCGAAACCAGAATGTa          <  2:221624/140‑1 (MQ=255)                                                                                                                                            gttgACCCACCCCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGATATGGGCAAGTTGGAAGCCGTGTTGGCGAAACCAGAATGTaaa        <  2:1034427/149‑1 (MQ=255)                                                                                                                                                  ccACCCCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGATATGGGCAAGTTGGAAGCCGTGTTGGCGAAACCAGAATGTAAAAtt     <  1:267131/148‑1 (MQ=255)                                                                                                                                                  ccACACCCCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGATATGGGCAAGTTGGAAGCCGTGTTGGCGAAACCAGAATGTAAAATTATg  <  1:522952/151‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                                 GTTTCTCGCGGCTATTGCCCACTGGTTTTCCACCCAGCATTACACCGCCATCGATTCTCAGACGGTGGTGTATGGCCCTTCTGTCATCTATATGGTTTCAGAACTGATTCGTCAGTGGTCTGAAA‑CAGGTGAAGGCGTGGTGATCCACACACCCGCCTATGACGCATTTTACAAGGCCATTGAAGGTAACCAGCGCACAGTAATGCCCGTTGCTTTAGAGAAGCAGGCTGATGGTTGGTTTTGCGATATGGGCAAGTTGGAAGCCGTGTTGGCGAAACCAGAATGTAAAATTATG  >  NC_000913/1701160‑1701454

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑