Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,576,077	0	C	A	42.9%	72.6 / 27.9	56	D515Y (GAT→TAT)	yddB	putative TonB‑dependent outer membrane receptor
Reads supporting (aligned to +/- strand):  ref base C (24/8);  new base A (0/24);  total (24/32)
Fisher's exact test for biased strand distribution p-value = 4.75e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGCGCAATAACGTTCTTACCGATTTTCTGCTGCAATCCCATTGCCAGTTCATCGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGACAGATAGTTGTCATAGTCATACCGCACGCCGGGC  >  NC_000913/1575928‑1576219                                                                                                                                                       |                                                                                                                                               aCGCGCAATAACGTTCTTACCGATTTTCTGCTGCAATCCCATTGCCAGTTCATCGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCa                                                                                                                                               <  2:184214/151‑1 (MQ=255)    cgcAATAACGTTCTTACCGATTTTCTGCTGCAATCCCATTGCCAGTTCATCGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCa                                                                                                                                               >  1:129934/1‑148 (MQ=255)               tCTTACCGATTTTCTGCTGCAATCCCATTCCCAGTTCATCGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGc                                                                                                                                  >  2:925846/1‑150 (MQ=255)                       tttttCTGCTCCAACCCCATGGCCATTTCATTTTTATAAGGCGTTTTAAAATCCTAATACCGCGTCATTTTTTTTTTACCTGATCCCAATCCCGTCCACTTATTGCGTATATCACGAAATCCAA‑AATAAAGAATATTCCCGCCATAGTa                                                                                                                           <  2:349958/148‑1 (MQ=255)                          ttCTGCTACAACCCCAGTGCAAGTTAATCGTTATAAGGCGTTTTAAAATCATGTTAACGCCTAAGATTTTTTTTCCCTGAAACCGTTCCCGCCCCGCTTTTGC‑GATTTTCGGAAAACCCATTAAAAAGAATATTCCCGCCATAGTAACgg                                                                                                                       <  2:484592/150‑1 (MQ=255)                               ctgcAATCCCATTCCCATTTCTTCTTTATAAGGCTTTTTCAAATCATGATAACGCGTTAGTTTTTTATTACCTTATACCTATCCCGCCCACCTATTGGGATTATCACTTAATCCAA‑TATAAAAAATTTTCCCGCCATAGTAACGGTta                                                                                                                    <  2:614452/148‑1 (MQ=255)                                  cAATCCCATTGCCAGTTCATCGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACct                                                                                                              >  1:786045/1‑151 (MQ=255)                                    accccATCGCCAATTATTCGTTATAAGGTTTTTTCAACTCCTAACAGCGCGACAGATTTTTCTTCCCTCCCACCGATTCCGCCCCCATTTTTGGGATTTCTAGTACTCCAA‑AATCAAGAATCTTTCCGCCATAGTAACGGTTATAACctg                                                                                                             <  1:515809/148‑1 (MQ=255)                                      cccATTGCCATTTCATCGTTATAAGGTTTTTTAAAATCTTGAAACCGCGTCAGATTTTTATTCCCTAATCCCGATTCCGTCCAGCTATTGCGAATATCCCGTAACCCAA‑TATAAAGAATATTCCCGCCATAGTAACGGTTATAACctgctg                                                                                                          <  1:309286/151‑1 (MQ=255)                                       ccATCGCCATTTCATCTTTATAAGGCTTTTTCAAATCCTGATAACGCGTCAGTTTTTTTTTCCCTAATACCAATTCCGCCCAGCTTTTGCGAATACCACGTAACCCCA‑TATCAAGAATATCCCCGCCATAGTAACGGTTATAAcc                                                                                                               <  2:376040/145‑1 (MQ=255)                                           tGCCAGTTCATCGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATc                                                                                                     >  2:927842/1‑151 (MQ=255)                                                 ttCATTTTTATAAGGTTTTTTCAAACCTTAATGACGCGTAAGATTTTTTTTCCCTGATCCCGATTCCTCCCAGTTATTGCGGATTTCACGTAATCCAA‑TATAAAAATTTTTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCAtt                                                                                                  <  2:826628/148‑1 (MQ=255)                                                        ttATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGAt                                                                                        >  1:126687/1‑151 (MQ=255)                                                        ttATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGAt                                                                                        >  1:303140/1‑151 (MQ=255)                                                           taAGGGGTTTTAAATTCATGATAGCGCGTGAGATTTTTATTCCCTAACACCGATCCCGTCCAGCTTTTGCGGATATCACATAATCCCA‑TAGCAAGAATTTCCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTa                                                                                      <  1:24319/150‑1 (MQ=255)                                                            aaggttttttAAACTCCTGATAGCGGGTGGGATTTTTATTCCCTGATACCTATTCCGTCCAGCTATTGCGAATATCACGTAACCCAA‑TATAAAAAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTa                                                                                      <  2:951066/143‑1 (MQ=255)                                                            aaGGCGTTTTAAAATCCTGAAACCGCTTCAGTGTTTTATTCCCTGATCCCGATTCCGCCCAGCTTTTGCGGATATCACGTAACCCCA‑TATAAAAAATTTTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGc                                                                                    <  1:647147/151‑1 (MQ=255)                                                              ggCTTTTTCAAATCCTGATACCGCGTCAGTTTTTTATTCCCTGATCCCGATCCCGCCCAGTTATTGCGGATATCACGTAACCCCA‑TAAAAAAAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCa                                                                                   <  1:431105/150‑1 (MQ=255)                                                                  ttttAAATTCCTAAAAACGCGTCAGTTTTTTATTCCCTAATCCCGATTCCGCCCAGCTATTGCGTATATCACTTAACCCCA‑TAAAAAAAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCaaaa                                                                                <  2:134434/149‑1 (MQ=255)                                                                          tccagaaaccgctccAGTGTTTTATTCCTTTATAACTATCCCTTCCGTCTTTTGTGGATCTCCCATAACCTCA‑TATAAATAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATccc                                                                         <  2:649275/134‑1 (MQ=255)                                                                          tCCTGATAACGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCAtt                                                                      >  1:729935/1‑151 (MQ=255)                                                                           cgtGATACCGCGTAAGATTTTTTTTCCCTAATACCTATCCCGTCCATCTTTGGCGTATATCACTTAACCCAA‑TATAAAAAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCAtt                                                                      <  2:514402/148‑1 (MQ=255)                                                                               aTACCGCGTAAGTTTTTTATTCCCTAATCCCGTTCCCGTCCAGCTATTGCGGATATCCCTTAACCCCA‑TATCAAGAATTTTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGt                                                                  <  1:470330/150‑1 (MQ=255)                                                                                 aaCGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCAt                                                               >  2:767345/1‑151 (MQ=255)                                                                                 aaCGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCAt                                                               >  1:443609/1‑151 (MQ=255)                                                                                 aaCGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCAt                                                               >  1:210660/1‑151 (MQ=255)                                                                                    gcgTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATaa                                                             >  1:189401/1‑150 (MQ=255)                                                                                     cgTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATaa                                                             >  1:602489/1‑149 (MQ=255)                                                                                      gtgatagTTTTATTACCTGATACCTTTTCCGCCCGTTTTTGGCGGATTTCACATAATCCAA‑TAAAAAGATTATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATaaa                                                            <  1:597311/144‑1 (MQ=255)                                                                                      gTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAgc                                                          >  1:430599/1‑151 (MQ=255)                                                                                       tCAGATTTTTTTTCCCTGATCCCGATCCCGCCCAGCTATGGCGAATATCACATAACCCCA‑TATAAAAAATTTTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAgc                                                          <  1:129030/150‑1 (MQ=255)                                                                                         agatTTTTATTCCCTGATCCCGTTTCCGTCCAGCTTTTGGGGATATCACGTAACCCCA‑TATAAAAAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAgcg                                                         <  2:831507/149‑1 (MQ=255)                                                                                              tttATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCgggg                                                    >  2:250584/1‑149 (MQ=255)                                                                                                  ttcccTGATACCGATTCCGCCCAGTTATTGCGAATATCACGTAACCCAA‑TATAAAAAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGat                                                <  1:331223/146‑1 (MQ=255)                                                                                                   tcccTGATCCCTATTCCGTCCATTTTTTGCGAATATCACGTAATCCAA‑TAAAAAAATTATCCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGatat                                              <  2:901767/148‑1 (MQ=255)                                                                                                    aCCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATtg                                            >  1:639808/1‑151 (MQ=255)                                                                                                     ccTGATCCCTATTCCGCCCAGCTATTGCGGATACCACTAAACCCCA‑TACAAAAAATATCCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATAtt                                             <  1:886311/149‑1 (MQ=255)                                                                                                     ccTAATCCCGATCCCGCCCATTTATTGCGGATATCACGTAACCCCA‑TATAAAAAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATAtt                                             <  1:596276/149‑1 (MQ=255)                                                                                                        gATCCCGATTCCGTCCAGCTATTGCGGATATCACGTAACCCAA‑TATCAAAAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATtgt                                           <  1:271274/148‑1 (MQ=255)                                                                                                         aTACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGtt                                       >  1:595064/1‑151 (MQ=255)                                                                                                            ccGATTCCGTCCAGCTTTTGCGGATATCACTTAACCCCA‑TAACAAAAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTgg                                         <  1:309072/146‑1 (MQ=255)                                                                                                            ccGATTCCGCCAAGCTATTGCGGATATCACGTAACCCCT‑TAAAAAAAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGa                                    <  1:692816/151‑1 (MQ=255)                                                                                                              gATTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGa                                    >  2:671647/1‑149 (MQ=255)                                                                                                               aTTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGAc                                   >  2:407224/1‑149 (MQ=255)                                                                                                                  ccGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGACAGAt                               >  1:400274/1‑150 (MQ=255)                                                                                                                    gTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGACAGATAGt                            >  1:603355/1‑151 (MQ=255)                                                                                                                       cAGCTATTGCGAATATCACGTAATCCAA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGACAGATAGTTgt                         <  2:335187/151‑1 (MQ=255)                                                                                                                        acttATGGCGAATATCACATAACCCAA‑TAAAAAAATTATCCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGACAGATAGTTgtc                        <  2:152848/148‑1 (MQ=255)                                                                                                                             ttGCGGATATCACTAACTCCAA‑AATAAAAAATATCCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGACAGATAGTTgtcatag                    <  2:828974/150‑1 (MQ=255)                                                                                                                               gCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGACAGATAGTTgtcatagtc                  >  1:61378/1‑150 (MQ=255)                                                                                                                                cGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGACAGATAGTTgtcatagtcat                >  1:170888/1‑151 (MQ=255)                                                                                                                                 ggATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGACAGATAGTTgtcatagtcat                >  1:21767/1‑150 (MQ=255)                                                                                                                                   atatCCCGTAATCCCA‑AATAAAAAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGACAGATAGTTGTCATAGTCATAc              <  2:93272/150‑1 (MQ=255)                                                                                                                                         cgaaacccaa‑tatAAAAAATATCCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGACAGATAGTTGTCATAGTCATACCGCa          <  2:154016/139‑1 (MQ=255)                                                                                                                                               cccA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGACAGATAGTTGTCATAGTCATACCGCACGCCGGGc  >  1:346095/1‑150 (MQ=255)                                                                                                                                               cccA‑TATAAAAAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGACAGATAGTTGTCATAGTCATACCGCACGCCg     <  1:952053/147‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                               ACGCGCAATAACGTTCTTACCGATTTTCTGCTGCAATCCCATTGCCAGTTCATCGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGATACCGATTCCGTCCAGCTATTGCGGATATCACGTAATCCCA‑TATCAAGAATATTCCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGACAGATAGTTGTCATAGTCATACCGCACGCCGGGC  >  NC_000913/1575928‑1576219

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑