Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,337,723	0	A	C	40.8%	75.3 / 12.5	50	G566G (GGT→GGG)	gyrA	DNA gyrase (type II topoisomerase), subunit A
Reads supporting (aligned to +/- strand):  ref base A (23/6);  new base C (0/20);  total (23/27)
Fisher's exact test for biased strand distribution p-value = 1.63e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGCCACGAGTGGCTTCCGGCAACTGATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTTCGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGCGGTGATTTCAGTACGACGT  >  NC_000913/2337580‑2337873                                                                                                                                                |                                                                                                                                                       gcgcCACGAGGGGCCTCCGGCAACTGATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTTCGCCACCAGCAGTCGGTCGATCAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTcc                                                                                                                                                 >  2:364673/1‑151 (MQ=255)  cgcCACGAGTGGCTTCCGGCAACTGATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTTCGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTccc                                                                                                                                                <  2:394525/151‑1 (MQ=255)                tCCGGCAACTGATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTTCGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTgcg                                                                                                                                  >  1:380923/1‑151 (MQ=255)                      aaCTGATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTTCGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGt                                                                                                                            >  1:177337/1‑151 (MQ=255)                         tGATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTTCGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTAtt                                                                                                                         >  2:513176/1‑151 (MQ=255)                          gATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTTCGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTc                                                                                                                        >  2:206572/1‑151 (MQ=255)                           aaaaaCTTTCATCGAATGGACGCGCCCCCGGCGGGAGAAGCACAAAATATGGTCGTGGGTTTCCGCCCCCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATCCGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTc                                                                                                                        <  2:871521/148‑1 (MQ=255)                           aTAAACTTTCATCGAATAGACGCGACCACGGCTGGAAAAGCAAAGAATATGGTCGTGATTTTTCGCCCCCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTCCCTTCCCCGCCACGACGCTGCGCTTCGTAtt                                                                                                                         <  2:191447/149‑1 (MQ=255)                             aaaCTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTTCGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTc                                                                                                                        >  1:11002/1‑148 (MQ=255)                              atcTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCAAAGAATATGGTCGTGGGTGTCCGCCACCAGAAGTCGGTCGATAAAGTCTTCTTCTTTAATCCGTGCGGCAGTTTTCCCTTCCCCGCCACGACGCTGCGCTTCGTATTCAg                                                                                                                      <  2:891682/147‑1 (MQ=255)                                    cATCGAATAGCCGCGCCCCCGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTTCGCCCCCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCgg                                                                                                               <  2:213348/150‑1 (MQ=255)                                     agcGAATAGCCGCGACGACGGCTGGAGAAGAACAGAATATGGTCGGGAGTGTCCGCCACCGGCTGTCGGTCGATAAAGCCTTCTTCTTTAAGACGTGGGGAAAATTTCCCTTCCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCgg                                                                                                               <  2:738101/147‑1 (MQ=255)                                      tCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGGCGTGAGTGATCGCCACCAGCAGTCGGTCGATAAAGTCTTTTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACCACGCTGCGCTTCGTATTTAGAAAGCGGCTg                                                                                                            >  2:698349/1‑151 (MQ=255)                                        gAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTGGGGAGTGTTCGCCCCCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATCCGTGCGGCAGTTTTCCCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTg                                                                                                            <  1:300771/149‑1 (MQ=255)                                             gACGCGACCACGGCGGGAGAAGCACAAAATATGGTCGTGAGTTTTCCCCCCCAGCAGTCGTTCGATAAAGTCTTCTTCTTTAATCCGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACtt                                                                                                      <  1:908819/150‑1 (MQ=255)                                               cgcgACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTTCGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAAc                                                                                                   >  1:440450/1‑151 (MQ=255)                                                gcgACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTTCGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACg                                                                                                  >  1:895078/1‑151 (MQ=255)                                                   aCCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTTCGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGt                                                                                                 >  2:171895/1‑149 (MQ=255)                                                    ccgcggcggGAGAAGCACAGAATATGTTCGTGGGTTTCCCCCACCAGCAGTCGGTCAAAAAATTCTTTTTCTTTAATACGTGCGGCAGTTTTCCCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTaa                                                                                                    <  2:408079/142‑1 (MQ=255)                                                    ccAGGGCGGGAGAAGCACAAAATATGGTCGGGAGTGTCCCCCCCCAGCAGTCGGTCGATAAAGTCTTCTTTTTTAATACGTGCGGCAGTTTTCCCTTCCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTa                                                                                                <  1:566736/149‑1 (MQ=255)                                                         gCTGGAGAAGCACAGAATATGGTCGTGAGTGTTCGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTgg                                                                                         >  2:13977/1‑151 (MQ=255)                                                           tGGAGAAGCACAGAATATGGTCGTGAGTGTTCGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTg                                                                                       >  1:788302/1‑151 (MQ=255)                                                                aaGCACAGAATATGGTGGTGAGTGTTCGCCCCCAGCGGTCGGTCGATAAAGTCTTCTTTTTTAATACGTGCGGCAGTTTTCCTTTCCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTgagaga                                                                                  <  1:519363/151‑1 (MQ=255)                                                                    aaaGAATTTGGTGGGGAGTTTCCCCCCCCAGCAGTGGGTGGAAAAATTTTTCTTCTTTAATGCGTGGGGAAGATTTCCTTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGc                                                                                <  2:630769/147‑1 (MQ=255)                                                                      aGAATATGGTCGTGAGTTTCCGCCACCAGCAGTCGGTCAAAAAAGTCTTCTTTTTTAATCCGTGCGGCAGATTTCCCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGc                                                                                <  1:857998/147‑1 (MQ=255)                                                                        aaTATGGTCGTGAGTGTCCGCCCCCAGCAGTCGGTCAATAAAGTCTTTTTCTTAAATACGGGCGGCAGATTTCCCTTCCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCa                                                                            <  1:56737/149‑1 (MQ=255)                                                                          tatGGTCGTGAGTGTTCGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGAc                                                                        >  1:845185/1‑151 (MQ=255)                                                                             ggTCGTGAGTGTGCGCCCCCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGTTTTCCCTTCCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGAc                                                                        <  2:433634/148‑1 (MQ=255)                                                                                  tGAGTGTTCGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCtt                                                                >  1:890551/1‑151 (MQ=255)                                                                                        ttCGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTgg                                                           <  2:320441/150‑1 (MQ=255)                                                                                            cccccaccgtccggtggATAAATTCTTCTTTTTTAATCCGTGGGGCAGATTTCCCTTCCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTg                                                        <  2:91461/138‑1 (MQ=255)                                                                                              accaGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATc                                                     >  2:830131/1‑150 (MQ=255)                                                                                                   cagTCGGTCGATAAAGTCTTCTTCTTTAATACGTGGGGCATATTTCCCTTCCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCt                                               <  1:87970/151‑1 (MQ=255)                                                                                                      tcggtcgATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTcc                                            >  1:917352/1‑151 (MQ=255)                                                                                                       cggtcgATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTcc                                            >  2:510014/1‑150 (MQ=255)                                                                                                        gttcgATAAATTTTTCTTCTTTAATGCGTGCGGGATATTTGCCTTGGCCGCGACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCGCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCat                                          <  2:410827/149‑2 (MQ=255)                                                                                                        ggtcgATAAAGTTTTCTTCTTTAATGCGTGCGGCATATTTCCCTTCCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCa                                           <  1:132983/150‑1 (MQ=255)                                                                                                         gtcaATAAATTCTTCTTCTTTAATACGTGCGGCAGTTTTCCCTTCCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCa                                           <  2:258218/149‑1 (MQ=255)                                                                                                               aaaGTCTTCTTTTTTAATGCGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTg                                      <  2:912353/148‑1 (MQ=255)                                                                                                                     ttcttcttTAATACGTGCGGCAGATTTCCCTTCCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTgc                              <  1:884429/150‑1 (MQ=255)                                                                                                                               aTACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGCgg                   >  1:181260/1‑151 (MQ=255)                                                                                                                                  cGTGCGGAATTTTTCCCTTCCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGCGGTg                 <  1:475839/150‑1 (MQ=255)                                                                                                                                   gTGCGGCATTTTTCCCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGCGGt                  <  1:334437/148‑1 (MQ=255)                                                                                                                                     gCGGCAGTTTTCCCTTCCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGCGGTGAttt             <  2:923833/151‑1 (MQ=255)                                                                                                                                          aGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGCGGTGATTTCa           >  2:787396/1‑148 (MQ=255)                                                                                                                                          aGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGCGGTGATTTCAGt         >  1:451782/1‑150 (MQ=255)                                                                                                                                            aTTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGCGGTGATTTCAGTacg      >  1:641255/1‑151 (MQ=255)                                                                                                                                             tttCCCTTGCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGGCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGCGGTGATTTCAGt         <  2:320101/147‑1 (MQ=255)                                                                                                                                             attACATTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGACAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTGGATGTCTGCGCTGTTGGCGGTGCTTTCAGt         >  2:158804/2‑147 (MQ=255)                                                                                                                                              ttACCTTTTCCGCCACGACGATGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTTCAGGTTGATGTCTGCGCTGTTGGCGGTGATTTCAGTacga     >  2:696942/1‑150 (MQ=255)                                                                                                                                                aCCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGCGGTGATTTCAGTACGACGt  >  2:931277/1‑151 (MQ=255)                                                                                                                                                |                                                                                                                                                       GCGCCACGAGTGGCTTCCGGCAACTGATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTTCGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGCGGTGATTTCAGTACGACGT  >  NC_000913/2337580‑2337873

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: ‑