Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,443,277	0	A	C	44.6%	93.7 / 15.4	56	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
Reads supporting (aligned to +/- strand):  ref base A (29/2);  new base C (0/25);  total (29/27)
Fisher's exact test for biased strand distribution p-value = 6.30e-14
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGCATAGAGTAACACATAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAAATACTAATACTG  >  NC_000913/3443131‑3443427                                                                                                                                                   |                                                                                                                                                       aCGCATAGAGTAACACATAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTAcccc                                                                                                                                                    <  2:445107/151‑1 (MQ=255)  cGCATAGAGTAACACATAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTAccccc                                                                                                                                                   <  1:1028096/151‑1 (MQ=255)    cATAGAGTAACACATAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGc                                                                                                                                                 >  1:997171/1‑151 (MQ=255)     aTAGAGTAACACATAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGcc                                                                                                                                                >  1:120433/1‑151 (MQ=255)               acaTAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACtt                                                                                                                                      >  1:138772/1‑151 (MQ=255)                caTAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACttt                                                                                                                                     >  1:129248/1‑151 (MQ=255)                     aGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCg                                                                                                                                >  1:1054790/1‑151 (MQ=255)                       cGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGt                                                                                                                              >  2:882856/1‑151 (MQ=255)                        ggTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGt                                                                                                                              >  2:379047/1‑150 (MQ=255)                        ggTTGCCCAGGCTGAAAATACAGAGAATTTTTTGTCGGCCAGTCCCACCCAGTCCCGCCCCCGAACCATGACGCGGTGGCCCCCGGAAAAAAAAAAATCCTGGAAGCGAAGTTTGCGGGGATTCCCCCCGCCATATTCACTTTCAGc                                                                                                                                 <  1:937797/147‑1 (MQ=255)                          tgccccGGGCTAAAAATACAGAAAATTTGTTGCCAGCCATTCCCACCCATTCCCCCCCCCGAACCATGCCGGGATGTCCGCGGGAAAAAAAATAATCCTGAAAGCAAAGATGGCCGGGTTTCCCCCCGCCATATTCACTTTCAGCGGTa                                                                                                                             <  1:254409/146‑1 (MQ=255)                              ccgggCTGAAAATACAGCAAATTTTTTGTCAGCCGGTCCCACCCAGTCCCCCCCCCGAACCATGAGGCGATGGTCGCGGGAAACAAAATAATACTGGAAGCGAAGATTGCGGGGATTCCCCCCGCCATATTCACTTTCAGCGGTAAAt                                                                                                                          <  1:179073/145‑1 (MQ=255)                                 ggCTACAAATACAGCAAATTTGTTGTCAGCCAGTTCCACCCAGTCCCGCCCCCAAACCATGCCGCGATGGCCGCCGGAAAAAAAATAATCCTGGAAGCGAAGTTGGCGGGGTTTCCCCCCGCCATATTCACTTTCAGCGGTAAAtgtgt                                                                                                                      <  1:170584/149‑1 (MQ=255)                                    tGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGctct                                                                                                                 >  1:708963/1‑151 (MQ=255)                                      aaaaaACAGCAAATTTGTTGCCAGCCATTCCCAACCAGTCCCCCCCCCGAACCATGACGCGATGGTCGCCGGAAAAAAAATAATACGGGAAGCGAAGATTGCCGGGATTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGctct                                                                                                                 <  1:166105/148‑1 (MQ=255)                                                gAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCAt                                                                                                        >  1:663231/1‑148 (MQ=255)                                                 aaaTTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGac                                                                                                    >  1:342549/1‑151 (MQ=255)                                                            aGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCtt                                                                                         >  1:550937/1‑151 (MQ=255)                                                             gcgaatgcaaaCCATTACCGCCCCCAAACCCTGCCGGGCGGCTCGCCGGAAAAAAAAGAATAGCGGAAAGAAGGATCGCTGGAATCCCCACCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGAcc                                                                                           <  1:860974/139‑1 (MQ=255)                                                             gCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTg                                                                                        >  1:1024153/1‑151 (MQ=255)                                                              ccttttCCACCCAGCCCCGCCCCCAACCCAGGCGGTGATGCGCGCGGGAAAAAAAATAATACTGAAAGGAAAGTTTGCCGTGTTCCCCCCCGCCATATTCACCTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGc                                                                                       <  2:23294/147‑1 (MQ=255)                                                               catttCCAACCAGTCCCCCCCCCGAACCATGGCGCGAGGGTCGCGGGGAAAAAAAAAATACTGGAAGCGAAGATGGCCGGGATTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACgacgac                                                                                            <  1:1095216/142‑1 (MQ=255)                                                                 gtcccACCCAGCCCCGCCCCCGAACCATGCCGCGTGGGCCGCCGGAAAAAAAATAATACTGAAGGGGAAGTTTGCGGGTTTTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCt                                                                                      <  2:1044204/146‑1 (MQ=255)                                                                      acccAGTCCCCCCCCCGACCCATGCCGCGATGGTCGCCGGAAACAAAATAATACGGGAAGCGAAGATGGCGGGTATTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGtt                                                                                <  1:509114/148‑1 (MQ=255)                                                                          aGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTcgcg                                                                           >  2:876331/1‑151 (MQ=255)                                                                            tcccGCCCCCGCTCAAGGCCGCGGTGGTCGCCGGAACAAAAATACAACGGAAAGCAAAGATCGCGGGGATCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTcgcg                                                                           <  2:568497/147‑1 (MQ=255)                                                                              ccGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGt                                                                       >  1:998049/1‑151 (MQ=255)                                                                              ccGCCCCCGAACCAGGACGGGATGGCCGCCGGAAAAAAAAAAATACTGGAAGCGAAGATTGCCGGGATTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAg                                                                        <  1:1038015/150‑1 (MQ=255)                                                                                   cccGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTAcc                                                                  >  2:989960/1‑151 (MQ=255)                                                                                       acccATGCCGGGATGGTCGCGGGAAACAGAAAAATCCGGGAAGCGAAGATTGCCGGATTTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACcaca                                                               <  1:362321/148‑1 (MQ=255)                                                                                       aacaagaagaggtgggTGGCCGGAAAAAAAATAATCTGGGAATCGAATATTGCCGGATTTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACaa                                                              <  2:925133/137‑1 (MQ=255)                                                                                             gACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATgcggc                                                        >  1:400251/1‑151 (MQ=255)                                                                                                gcgAGGGCCGCGGGAAATAAAATAATACTGGAAGCGAAGTTTGCCGGTTTCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATgcggcg                                                       <  2:173261/149‑1 (MQ=255)                                                                                                     ggTCGCCGGAAACAAAATAATACTGGAAGCGAAGTTTGCGGGTTTTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGAcc                                                 <  1:177644/150‑1 (MQ=255)                                                                                                           cGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTc                                           >  1:446206/1‑150 (MQ=255)                                                                                                            gggAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTca                                          >  1:5974/1‑150 (MQ=255)                                                                                                            gggAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTAACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTca                                          >  1:122851/1‑150 (MQ=255)                                                                                                               aaCAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTcaaca                                       >  2:903458/1‑150 (MQ=255)                                                                                                               aaCAAAATAATCATGAAGGCAAATTTTGGCGGGATCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTcaacaa                                      <  2:1002679/151‑1 (MQ=255)                                                                                                                aCAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTcaacaa                                      >  1:654851/1‑150 (MQ=255)                                                                                                                 cAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAAt                                    >  1:377483/1‑151 (MQ=255)                                                                                                                    aaaaataCGGGAAGCGAAGTTTGCCGGGATTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATaca                                 <  1:916295/148‑1 (MQ=255)                                                                                                                             ggAAGCAAAGATTGCCGGGTTCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAAc                        <  1:95515/151‑1 (MQ=255)                                                                                                                               aggggAAGATGGCGGGTATCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAg                           <  1:246560/142‑1 (MQ=255)                                                                                                                               agggaagtaTTGCGGGTATTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGt                      <  2:1076314/143‑1 (MQ=255)                                                                                                                                   gAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGTCCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACt                  >  1:809651/1‑151 (MQ=255)                                                                                                                                   gAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACt                  >  2:933129/1‑151 (MQ=255)                                                                                                                                    aaGATTGCCGGGATCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTg                 <  1:583762/151‑1 (MQ=255)                                                                                                                                    aaGATGGCCGGGATTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTc                     <  1:45934/147‑1 (MQ=255)                                                                                                                                      gATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGc                >  2:817455/1‑150 (MQ=255)                                                                                                                                       aTTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCa               >  1:150735/1‑150 (MQ=255)                                                                                                                                           cggggATCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAaat            <  2:1117902/147‑1 (MQ=255)                                                                                                                                           ccGGGCTTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAaata           <  1:864759/150‑1 (MQ=255)                                                                                                                                             gggATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAaatact         >  1:1081937/1‑150 (MQ=255)                                                                                                                                             gggATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAaatact         >  2:264910/1‑150 (MQ=255)                                                                                                                                                  tACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAaatactaatact   >  1:612956/1‑151 (MQ=255)                                                                                                                                                   aCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAAATACTAATACTg  >  2:64315/1‑151 (MQ=255)                                                                                                                                                   |                                                                                                                                                       ACGCATAGAGTAACACATAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAAATACTAATACTG  >  NC_000913/3443131‑3443427

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑