Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,621,118	0	A	C	43.6%	76.7 / 10.1	55	V7G (GTG→GGG)	eamA	cysteine and O‑acetyl‑L‑serine efflux system
Reads supporting (aligned to +/- strand):  ref base A (21/10);  new base C (0/24);  total (21/34)
Fisher's exact test for biased strand distribution p-value = 7.66e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TACTTTCGGTCGTGCGACAAAAAAGATAGCCGGAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGTCGCTATACTTCGGATTTT  >  NC_000913/1620970‑1621268                                                                                                                                                     |                                                                                                                                                       tACTTTCGGTCGTGCGACAAAAAAGATAGCCGGAAAAGCGATCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACAcc                                                                                                                                                      >  2:1068994/1‑151 (MQ=255)        ggTCGTGCGACAAAAAAGATAGCCGGAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCtt                                                                                                                                               <  2:1029321/151‑1 (MQ=255)         gTCGTGCGACAAAAAAGATAGCCGGAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCttt                                                                                                                                              >  1:816749/1‑151 (MQ=255)                gACAAAAAAGATAGCCGGAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGAc                                                                                                                                       >  1:561279/1‑151 (MQ=255)                  cAAAAAAGATAGCCGGAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACAt                                                                                                                                     >  1:1087996/1‑151 (MQ=255)                     aaaaGATAGCCGGAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCt                                                                                                                                  <  1:1070793/151‑1 (MQ=255)                     aaaaGATAGCCGGAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCt                                                                                                                                  <  1:729323/151‑1 (MQ=255)                         gATAGCCGGAAAAGCGACCAGCATAAAGCGCAAACCGTCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTAcc                                                                                                                               >  1:139381/1‑150 (MQ=255)                                   aaaGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACCCCCCATCTTTTCGCGACATTCTACCGCCTCTGAAtt                                                                                                                    <  1:1031316/151‑1 (MQ=255)                                          ccAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCtt                                                                                                             >  1:1106035/1‑151 (MQ=255)                                          ccAACAAAAAGCCCAACCCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATCCGCCCACTCCCAGTAGCGCCAACCCCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTc                                                                                                                  <  1:892452/146‑1 (MQ=255)                                              cATAAAGCGCAAACCGGCCAGCATCAGCGGGGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGt                                                                                                         >  2:969509/1‑151 (MQ=255)                                               aaaaaGCGAAACCCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTACCCCCCATACGACCCCTCCCATTAGCGCCAACATCCCATCTTTCCGCGACTTTCTACCGCCTCTGAATTTCATCTTTTGt                                                                                                         <  1:968163/148‑1 (MQ=255)                                               aTAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGt                                                                                                         >  1:334694/1‑150 (MQ=255)                                               aTAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCAAAAAATTTACCCCCCATACGCCCCCTCCCAGTAGCCCCAACCCCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTg                                                                                                          <  1:827008/149‑1 (MQ=255)                                               aTAAAGCGCAAACCGCCCAGCATCAGCGGTGGCTTGTTATAAAGCCCCACTTTGATGACCAAAAAATTTAGCCCCCATACGACCACTCCCAGTAGCGCCAACCCCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGt                                                                                                         <  2:983685/150‑1 (MQ=255)                                               aTAAAGCGAAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCAATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTTTACCGCCTCTGAATTTCATCTTTTg                                                                                                          <  2:1214621/149‑1 (MQ=255)                                                     cgcAACCCGCCCAGCATCAGCGGTGGCATGTAATGAACCCCCACTTTGATGCCCAAAAAATTTACCCCCCATACGCCCCCACCCATTAGCGCCAACCCCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCaa                                                                                                   <  1:967576/150‑1 (MQ=255)                                                        aacccGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGCCCACTACCAGTAGCGCCAACCCCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCa                                                                                                <  2:626942/147‑1 (MQ=255)                                                        aaaCCGGCCAGCATCAGCGGTGGCCTGTTATGACGCCCCACTTTGATGACCCCAAAATTTAGCCCCCATACCACCACTCCCAGTCGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCa                                                                                                <  2:709007/150‑1 (MQ=255)                                                           ccGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCATTTTGATGACCACAAAATTTACCCCCCATACACCCCCTACCAGTAGCGCCAACCCCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACt                                                                                             <  2:245702/150‑1 (MQ=255)                                                           ccGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACtt                                                                                            >  2:437479/1‑151 (MQ=255)                                                                cagcagCGGCGGTGGCATGTTAAAAAGCCCCACTTTGAGAACCAAAAAATTTAGCCCCCATACGCCCCCTCCCAGAAGCGCAAACCCCCCATTTTTCCCCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAg                                                                                          <  1:136208/148‑1 (MQ=255)                                                                 aGCATCAGCGGTGGCATTTTATGAAGCCCCCCTTTGATGACCACAAAATTTAGCCCCCATACGACCACTCCCAGTAGCGCCAACCCCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCt                                                                                        <  2:1049875/149‑1 (MQ=255)                                                                  gCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGa                                                                                      >  2:569449/1‑150 (MQ=255)                                                                       aGCGTTGGGATGTTACGAAGCCCCGTTTTAATGACCAAAAATTTAACCCCCCAGACGCCCACTCCCAGTGCCTCCAACCCCCCATTTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTAc                                                                                <  2:1138921/151‑1 (MQ=255)                                                                       aGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTAc                                                                                >  2:164071/1‑151 (MQ=255)                                                                       aGCGGGGGCATGTTAGGAAGCCCCACTTTGATGACCAAAAAATTTACCCCCCATCCGCCCACTCCAAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTa                                                                                 <  2:508170/150‑1 (MQ=255)                                                                                  gTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAAc                                                                     >  2:28708/1‑151 (MQ=255)                                                                                   ttATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAAc                                                                     >  1:46913/1‑150 (MQ=255)                                                                                   ttATGAAGCCCCACTTTGATGACCAAAAAATTTAGCCCCCATACGACCACTCCCAGTAGCGCCAACCCCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCttt                                                                        <  2:117546/147‑1 (MQ=255)                                                                                     aTGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGt                                                                  >  2:264926/1‑151 (MQ=255)                                                                                        aacccccACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTCCCAGTAGCCCCAACCCCCCATCTTTTCGCAACTTTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGtt                                                                 <  1:659377/146‑1 (MQ=255)                                                                                               aCTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGtt                                                         >  2:424233/1‑150 (MQ=255)                                                                                                 tttGATGACCACAAATTTTAGCCCCCATCCGCCCACTCCCAGTAGCCCCACCCCCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGtt                                                         <  1:1352/148‑1 (MQ=255)                                                                                                  ttGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTCGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGt                                                      >  2:533074/1‑150 (MQ=255)                                                                                                     atgaCCACAAAATTTAGCCCCCATACGCCCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGcc                                                  <  1:189409/151‑1 (MQ=255)                                                                                                             aaaaTTTAGCCCCCATACGACCACTCCCAGTAGCGCAAACCCCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTacga                                          <  2:599864/151‑1 (MQ=255)                                                                                                             aaaaTTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTacg                                           >  1:191566/1‑150 (MQ=255)                                                                                                                      cccccATCCCCCCACCACCATTACCGCCAACCCCCCATCTTTCCGCGACATTTTGCCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCAtt                                   <  1:25590/149‑1 (MQ=255)                                                                                                                       ccccATACGCCCACTACCAGTAGCGCCAACCCCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAAt                                <  2:561284/151‑1 (MQ=255)                                                                                                                          cATACGACCACTCCCAGTAGCGCCAACCCCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATgc                              <  2:441109/150‑1 (MQ=255)                                                                                                                          cATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATgcg                             >  1:511956/1‑151 (MQ=255)                                                                                                                          cATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATgcg                             >  2:48075/1‑151 (MQ=255)                                                                                                                                 ccatgcccAGTAGGACCAACCCCCCATCGTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCaa                          <  1:443170/141‑1 (MQ=255)                                                                                                                                 ccACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAAt                        <  2:843658/149‑1 (MQ=255)                                                                                                                                       ccAGTAGCGCCAACCCCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGt                    <  1:655817/147‑1 (MQ=255)                                                                                                                                       ccAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGTCGCt                >  2:202801/1‑151 (MQ=255)                                                                                                                                         aGTAGCGCCAACCCCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGTCGCtat              <  1:1101543/151‑1 (MQ=255)                                                                                                                                          gTAGCGCCACCCCCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGTCGCtata             <  2:59087/151‑1 (MQ=255)                                                                                                                                             gcgcCAACCCCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGTCGCTATACt           <  2:816755/150‑1 (MQ=255)                                                                                                                                                 cAACCCCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGTCGCtata             <  2:1188074/144‑1 (MQ=255)                                                                                                                                                  aaCCCCCCATATTTTCGCCACATTCTTCCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGTCGCTATACTTCg        <  1:671347/148‑1 (MQ=255)                                                                                                                                                  aaCACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGTCGCTATACTTCGGa      <  1:200631/150‑1 (MQ=255)                                                                                                                                                  aaCACCCAATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGTCGCTATACTTc         >  1:1156182/1‑147 (MQ=255)                                                                                                                                                    cacCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGTCGCTATACTTCGGAttt   >  2:961904/1‑151 (MQ=255)                                                                                                                                                     acCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGTCGCTATACTTCGGAtttt  >  1:1101829/1‑151 (MQ=255)                                                                                                                                                     |                                                                                                                                                       TACTTTCGGTCGTGCGACAAAAAAGATAGCCGGAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACATTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGTCGCTATACTTCGGATTTT  >  NC_000913/1620970‑1621268

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: ‑