Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,349,145	0	A	C	42.3%	85.1 / 14.7	52	F110V (TTC→GTC)	inaA	acid‑inducible Kdo/WaaP family putative kinase
Reads supporting (aligned to +/- strand):  ref base A (25/5);  new base C (0/22);  total (25/27)
Fisher's exact test for biased strand distribution p-value = 3.07e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATATGGCGAACATAACAACAGCCATGCTGACGATTAATGCTATGCATTTTCTTAAACGCCA‑GCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGA  >  NC_000913/2348996‑2349291                                                                                                                                                       |                                                                                                                                                   gATATGGCGAACATAACAACAGCCATGCTGACGATTAATGCTATGCATTTTCTTAAACGCCA‑GCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTCCATGCTGGGCATACCAGTCAGCAATGCTGATGaa                                                                                                                                                    <  2:617748/150‑1 (MQ=255)     tGGCGAACATAACAACAGCCATGCTGACGATTAATGCTATGCATTTTCTTAAACGCCA‑GCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAAcccc                                                                                                                                                >  2:418220/1‑150 (MQ=255)     tGGCGAACATAACAACAGCCATGCTGACGATTAATGCTATGCATTTTCTTAAACGCCA‑GCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCg                                                                                                                                               >  1:314256/1‑151 (MQ=255)      ggCGAACATAACAACAGCCATGCTGACGATTAATGCTATGCATTTTCTTAAACGCCA‑GCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCgt                                                                                                                                              <  1:753083/151‑2 (MQ=255)      ggCGAACATAACAACAGCCATGCTGACGATTAATGCTATGCATTTTCTTAAACGCCA‑GCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCg                                                                                                                                               <  2:180525/150‑1 (MQ=255)       gCGAACATAACAACAGCCATGCTGACGATTAATGCTATGCATTTTCTTAAACGCCA‑GCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGcc                                                                                                                                             <  1:439447/151‑1 (MQ=255)              tAACAACAGCCATGCTGACGATTAATGCTATGCATTTTCTTAAACGCCA‑GCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCtt                                                                                                                                      >  1:448093/1‑151 (MQ=255)                    caGCCATGCTGACGATTAATGCTATGCATTTTCTTAAACGCCA‑GCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTc                                                                                                                                 >  1:493883/1‑150 (MQ=255)                       ccATGCTGACGATTAATGCTATGCATTTTTTAAAACGCCA‑GCGCCCCTGCTTTAAACATGGTTTCCCTTACTTCGAAAAAAAAGGGCAATACTGCATGCGGGCCATCCCAACCAGCAATGCTGATAACCCCCGCCATATCTTCAGTCACCa                                                                                                                             <  2:291829/151‑1 (MQ=255)                       ccATGCTGACGATTAATGCTATGCATTTTCTTAAACGCCA‑GCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCAcc                                                                                                                              >  1:350640/1‑150 (MQ=255)                       ccATGCTGACGATTAATGCTATGCATTTTCTTAAACGCCA‑GCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCAcc                                                                                                                              >  2:199511/1‑150 (MQ=255)                         aTGCTGACGATTAATGCTATGCATTTTCTTAAACGCCA‑GCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGc                                                                                                                           >  1:163027/1‑151 (MQ=255)                           gCTGACGATTAATGCTATGCATTTTCTTAAACGCCA‑GCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCa                                                                                                                          >  1:873110/1‑150 (MQ=255)                             tggcgttaaaTGCTATGTATTTTCTTAACCGCCA‑CCGCGACGGCTTAAACCATGCCTTCCCATCTGTCGACAGAAAAAGGCGTTACGCGATGGGGTTCTTGCCAGTCAGAAATCTTAATACCCCCCGCCATATCTTCAGTCACCAg                                                                                                                            <  2:153777/138‑1 (MQ=255)                                 gATTAATGCTATGCATTTTCTTAAACGCCA‑GCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCg                                                                                                                   >  2:430306/1‑151 (MQ=255)                                       tgttATGCTTTTTCTCAACCGCCA‑CCGCCACTTTTTTCAACGTGGCTTGCCGTACTTCGTAAAAATAAGGCTATCCTCCATGCTGGGCATACCAGCAAGAATTGTTGATAACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCAtt                                                                                                              <  2:337568/147‑1 (MQ=255)                                        gCTATGCTTTTTCTAAAACGCCG‑GCGCCACTTCTTTCAACAGGGTTTGCCGTTCTTCGTCAGAAAAGGGCGATACGGCATGCGGGGCATACAAGTCAGAATTGGTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCa                                                                                                            <  1:325412/151‑1 (MQ=255)                                        gCTATGCATTTTCTTAAACGCCA‑GCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTc                                                                                                             >  2:801584/1‑150 (MQ=255)                                          tATGCTTTTTC‑TAAACCCCAGGCGCCCCGGCTTTAAACTGGGCTGTCCGTCCTCCGTAAAAAAAGGGCATTACTGCATGCGGGGAACCCCCGCGACAATTCCTGATAACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCAtt                                                                                                              <  2:456529/147‑1 (MQ=255)                                          tATGCATTTTCTTAAACGCCA‑GCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCAcc                                                                                                          >  1:271753/1‑151 (MQ=255)                                            tcttttttCTCAAGCCCCG‑CCGCCCCTGCTTTCAAATGGGCTGTCCGTTCTGAGTTAGAAAAAGGCCATTCTACTTGTGGGGCGTCCCGCACCACAAGCCTGTTAACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCAc                                                                                                           <  1:808304/144‑1 (MQ=255)                                            tGCTTTTTCTAAACCGCCA‑CCGCCACTGCTTTCAACATGGCTTGCCGTCCTTCGTAAGAAAAGGGCGATACTGCATGCTGGGCATCCCAGTCAGCAATGCTGAGGACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCAcc                                                                                                          <  1:295547/149‑1 (MQ=255)                                                        aaCGCCA‑GCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCg                                                                                            >  2:45876/1‑151 (MQ=255)                                                         aCGCCA‑GCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGc                                                                                           >  2:884406/1‑151 (MQ=255)                                                             cA‑GCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTc                                                                                        >  1:233420/1‑150 (MQ=255)                                                              ccgccccccttcTTTCAACAGGGTTTGCCGTCTTTCGAAAAAATAAGGCGATCCTGCATGCGGGGCACCCCAGTCAGCAATGCTAATAACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCtt                                                                                         <  2:847829/138‑1 (MQ=255)                                                                        gCTTTCAACATGGCTTGCCGTCCTTCGTAAAAATAAGGCAATACTGCATGCTGGGCATACCAGCCAGAAATGCTGATAACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACg                                                                              <  1:616075/150‑1 (MQ=255)                                                                            tCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCtt                                                                         >  2:108659/1‑151 (MQ=255)                                                                              aaCATGGCTTGCCTTACTTCGAAAGAAAAGGGCGATCCTGCTTGCGGGGCATCCCAGTAAGCAATGCTAATGACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCtt                                                                         <  1:336694/149‑1 (MQ=255)                                                                              aaCATGGCTTGCCGTTCTTCGTCAAAATAAGGCGATACTGCATGCTGGGCATCCCAGTCAGCAATGCTGATAACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGa                                                                             <  1:38346/145‑1 (MQ=255)                                                                              aaCATGGCTCCCCTTACTTCGTAAAAAAAGGGCGATCCTGCTTGCGGGCAATCCCAGCCAGAAATGCTGATGACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGa                                                                             <  2:61266/145‑1 (MQ=255)                                                                              aaCATGCTTTGCCGTCCTTCGTCATAAAAGGGCGATACGCCTTGCGGGCCATCCCAGTCAACAATGCTAATAACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCg                                                                       <  2:36256/151‑1 (MQ=255)                                                                                  tGGCTTGCTGTCCTCCGGAAAAATAAGGCGATCCTCCAGCTTGGGCATCCAAGCCAGCAATTCTGATGACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCa                                                                    <  1:493622/150‑1 (MQ=255)                                                                                      ttGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATg                                                               >  1:713084/1‑151 (MQ=255)                                                                                      ttGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATg                                                               >  1:812493/1‑151 (MQ=255)                                                                                            ttcTTCGTAAAAAAAAGGCGATCCTGCATGCGGGCCAACCCAGCAAAAAAGGCTGATAACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACAcc                                                          <  2:713391/148‑1 (MQ=255)                                                                                                  gaaaaaaaaaGGCGTTCCTGCATGCTGGGCATCCCAGTCAGCAATGCTAAAAACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATg                                                               <  2:7095/131‑1 (MQ=255)                                                                                                  gTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGt                                                   >  2:790803/1‑151 (MQ=255)                                                                                                     aGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTcc                                                >  2:929489/1‑151 (MQ=255)                                                                                                     aGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTcc                                                >  1:445618/1‑151 (MQ=255)                                                                                                             gCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCGCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCt                                          >  2:638685/1‑149 (MQ=255)                                                                                                               gATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGTCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTaa                                      <  2:260374/151‑1 (MQ=255)                                                                                                                atccTGCATGCGGGCCATACCAGCCAGAAATGCTGATAACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTaa                                      <  1:487304/147‑1 (MQ=255)                                                                                                                        tGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCa                              >  2:756955/1‑150 (MQ=255)                                                                                                                        tGCTGGCCATCCCAGACAGCAATGCTGATGACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCg                                <  1:598353/148‑1 (MQ=255)                                                                                                                          cTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAAcc                           >  2:370549/1‑151 (MQ=255)                                                                                                                            ggacATCCCAGTCACCAATGATGATGACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTc                         <  2:745513/148‑1 (MQ=255)                                                                                                                               cATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACg                      >  2:399889/1‑151 (MQ=255)                                                                                                                               cATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACg                      >  2:909394/1‑151 (MQ=255)                                                                                                                                     aGTCAGAAATGCTGATGACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACGGACAAt                <  1:906221/151‑1 (MQ=255)                                                                                                                                            attGCTGATGCCCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTg           <  2:109233/147‑1 (MQ=255)                                                                                                                                                cTGATGACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCg       <  1:302641/149‑1 (MQ=255)                                                                                                                                                   atgaCCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGa  <  1:129968/151‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                   GATATGGCGAACATAACAACAGCCATGCTGACGATTAATGCTATGCATTTTCTTAAACGCCA‑GCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGGCGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGA  >  NC_000913/2348996‑2349291

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑