Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	576,628	T→C	pseudogene (198/1040 nt)	nmpC ←	DLP12 prophage; putative outer membrane porin NmpC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	576,628	0	T	C	100.0%	207.3 / NA	57	pseudogene (198/1040 nt)	nmpC	DLP12 prophage; putative outer membrane porin NmpC
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (22/35);  total (22/35)

CGTAGTCACCGAATTTCAGGCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTTTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTACAGATCCAGCTTGTTACTGTCTTTATTATAAATTTCAGC  >  NC_000913/576495‑576756                                                                                                                                      |                                                                                                                                 cGTAGTCACCGAATTTCAGGCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCt                                                                                                                            >  2:728367/1‑140 (MQ=255) cGTAGTCACCGAATTTCAGGCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATCCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCt                                                                                                                            >  2:852687/1‑140 (MQ=255)        aCCGAATTTCAGGCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGc                                                                                                                     >  1:585957/1‑140 (MQ=255)        aCCGAATTTCAGGCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGc                                                                                                                     >  1:486836/1‑140 (MQ=255)          cGAATTTCAGGCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCa                                                                                                                   >  1:612863/1‑140 (MQ=255)             aTTTCAGGCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGa                                                                                                                <  2:82802/140‑1 (MQ=255)             aTTTCAGGCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGa                                                                                                                <  1:610618/140‑1 (MQ=255)             aTTTCAGGCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGa                                                                                                                <  2:757716/140‑1 (MQ=255)             aTTTCAGGCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGa                                                                                                                >  1:445195/1‑140 (MQ=255)             aTTTCAGGCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGa                                                                                                                <  2:445195/140‑1 (MQ=255)             aTTTCAGGCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGa                                                                                                                <  1:220141/140‑1 (MQ=255)             aTTTCAGGCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGa                                                                                                                <  1:728367/140‑1 (MQ=255)             aTTTCAGGCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGa                                                                                                                <  2:190555/140‑1 (MQ=255)               ttCAGGCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACg                                                                                                              <  2:585957/140‑1 (MQ=255)                 cAGGCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACggg                                                                                                            <  1:519920/140‑1 (MQ=255)                  agcccAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGc                                                                                                           <  1:175250/137‑1 (MQ=255)                  agcccAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGc                                                                                                           >  2:175250/4‑140 (MQ=255)                  aGGCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGa                                                                                                                <  1:631184/135‑1 (MQ=255)                  aGGCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGa                                                                                                                >  2:631184/1‑135 (MQ=255)                    gCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCAt                                                                                                         >  2:874671/1‑140 (MQ=255)                    gCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCAt                                                                                                         <  1:98018/140‑1 (MQ=255)                     ccAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATa                                                                                                        <  2:796790/140‑1 (MQ=255)                     ccAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATa                                                                                                        <  2:612863/140‑1 (MQ=255)                       aGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAag                                                                                                      >  2:29836/1‑140 (MQ=255)                        gCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAagt                                                                                                     >  2:313085/1‑140 (MQ=255)                           aaGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAagtagt                                                                                                  <  2:486836/140‑1 (MQ=255)                            aGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAgtagta                                                                                                 <  1:848927/140‑1 (MQ=255)                                          ttATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGc                                                                                   <  1:175509/140‑1 (MQ=255)                                               tttGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGcatcat                                                                              <  1:198138/140‑1 (MQ=255)                                                 tGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTa                                                                            >  2:446305/1‑140 (MQ=255)                                                  ggaggaACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTag                                                                           <  1:29836/140‑1 (MQ=255)                                                     ggaACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAgagg                                                                        <  2:738880/140‑1 (MQ=255)                                                           ttGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAagt                                                                  >  2:350833/1‑140 (MQ=255)                                                            tGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAagta                                                                 <  1:874671/140‑1 (MQ=255)                                                                          gTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTaa                                                   <  1:796150/140‑1 (MQ=255)                                                                          gTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTaa                                                   <  1:670128/140‑1 (MQ=255)                                                                            tGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACt                                                 <  1:446305/140‑1 (MQ=255)                                                                                   gAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGt                                          >  1:882682/1‑140 (MQ=255)                                                                                     aTTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTAc                                        <  1:286765/140‑1 (MQ=255)                                                                                        cATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTACAGa                                     <  1:350833/140‑1 (MQ=255)                                                                                         atatTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTACAGAt                                    <  2:873780/140‑1 (MQ=255)                                                                                            ttCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTACAGATCCa                                 <  1:852687/140‑1 (MQ=255)                                                                                              cccACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTACAGATCCAGc                               >  2:200465/1‑140 (MQ=255)                                                                                              cccACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTACAGATCCAGc                               >  2:646181/1‑140 (MQ=255)                                                                                               ccACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTACAGATCCAGCt                              <  2:492545/140‑1 (MQ=255)                                                                                                 aCTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTACAGATCCAGCTTg                            >  1:593670/1‑140 (MQ=255)                                                                                                  cTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTACAGATCCAGCTTGt                           <  1:200465/140‑1 (MQ=255)                                                                                                   tGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTACAGATCCAGCTTGtt                          >  1:64900/1‑140 (MQ=255)                                                                                                    gACCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTACAGATCCAGCTTGTTa                         <  1:848946/140‑1 (MQ=255)                                                                                                     aCCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTACAGATCCAGCTTGTTAc                        >  2:413440/1‑140 (MQ=255)                                                                                                     aCCGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTACAGATCCAGCTTGTTAc                        <  1:143717/140‑1 (MQ=255)                                                                                                      ccGAAACCAGTCAGTTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTACAGATCCAGCTTGTTACt                       <  1:413440/140‑1 (MQ=255)                                                                                                               gtcagtTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTACAGATCCAGCTTGTTACTGTCTttatt              >  2:851181/1‑140 (MQ=255)                                                                                                               gtcagtTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTACAGATCCAGCTTGTTACTGTCTttatt              >  2:577461/1‑140 (MQ=255)                                                                                                               gtcagtTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTACAGATCCAGCTTGTTACTGTCTttatt              >  1:962690/1‑140 (MQ=255)                                                                                                                  agtTGATCGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTACAGATCCAGCTTGTTACTGTCTTTATtata           <  1:851181/140‑1 (MQ=255)                                                                                                                         cGTTGATTTGGGTCTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTACAGATCCAGCTTGTTACTGTCTTTATTATAAATTTCa    <  1:646181/140‑1 (MQ=255)                                                                                                                           ttGATTTGGGTCTCCCCTTTGAAGCCAAGACGCGCATAAGCACCATCACCATCACCTGCATCATTCGAGGACAAGTAGTGCTCAGCATTACCTTCCCCCTACAGATCCACCTTGTTACTGCCTTTATTATAAATTTCAGc  <  2:962690/140‑1 (MQ=255)                                                                                                                                      |                                                                                                                                 CGTAGTCACCGAATTTCAGGCCAGCGAAGGCAAGACGGGTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCATATTCCCACTGACCGAAACCAGTCAGTTGATCGTTGATTTGGGTTTCACCTTTGAAGCCAAGACGGGCATAAGTAGTATCACCATCATCTGCATCATTAGAGGAGAAGTAGTGCTTAGCATTAACTTTCCCGTACAGATCCAGCTTGTTACTGTCTTTATTATAAATTTCAGC  >  NC_000913/576495‑576756

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑