Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,758,830	T→C	L63L (TTA→CTA)	alpA →	CP4‑57 prophage; DNA‑binding transcriptional activator AlpA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,758,830	0	T	C	100.0%	207.6 / NA	58	L63L (TTA→CTA)	alpA	CP4‑57 prophage; DNA‑binding transcriptional activator AlpA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (25/33);  total (25/33)

ACAGGTATGGCACGGGCCACCATCTATGACTGGTTGAACCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGTTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTAATAGCGGAATAGCCATATTTGCTAAACAATTTCTTAA  >  NC_000913/2758698‑2758961                                                                                                                                     |                                                                                                                                    aCAGGTATGGCACGGGCCACCATCTATGACTGGTTGAACCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATcaca                                                                                                                              <  2:348437/140‑1 (MQ=255)     gTATGGCACGGGCCACCATCTATGACTGGTTGAACCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGGATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGc                                                                                                                          >  2:247859/1‑140 (MQ=255)        tGGCACGGGCCACCATCTATGACTGGTTGAACCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGt                                                                                                                       >  2:455328/1‑140 (MQ=255)          gCACGGGCCACCATCTATGACTGGTTGAACCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTaa                                                                                                                     <  1:857471/140‑1 (MQ=255)            aCGGGCCACCATCTATGACTGGTTGAACCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAAc                                                                                                                   <  2:941432/140‑1 (MQ=255)                   accaTCTATGACTGGTTGAACCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTg                                                                                                            <  1:455328/140‑1 (MQ=255)                    ccaTCTATGACTGGTTGAACCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGa                                                                                                           <  2:966090/140‑1 (MQ=255)                     caTCTATGACTGGTTGAACCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAg                                                                                                          <  1:472075/140‑1 (MQ=255)                          aTGACTGGTTGAACCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGa                                                                                                           <  1:283075/134‑1 (MQ=255)                          aTGACTGGTTGAACCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGa                                                                                                           >  2:283075/1‑134 (MQ=255)                          aTGACTGGTTGAACCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGgtgt                                                                                                     >  2:702312/1‑140 (MQ=255)                          aTGACTGGTTGAACCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGgtgt                                                                                                     >  1:722199/1‑140 (MQ=255)                          aTGACTGGTTGAACCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGgtgt                                                                                                     <  1:702312/140‑1 (MQ=255)                               tGGTTGAACCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACAt                                                                                                <  1:317361/140‑1 (MQ=255)                               tGGTTGAACCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACAt                                                                                                >  2:449980/1‑140 (MQ=255)                                 gTTGAACCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGa                                                                                              >  2:337671/1‑140 (MQ=255)                                 gTTGAACCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGa                                                                                              >  1:924277/1‑140 (MQ=255)                                  ttGAACCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGaa                                                                                             >  2:641849/1‑140 (MQ=255)                                     aaCCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTc                                                                                          >  1:523061/1‑140 (MQ=255)                                                    cgatacgatGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGt                                                                           >  2:620063/1‑140 (MQ=255)                                                        acgatGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATc                                                                       <  2:924277/140‑1 (MQ=255)                                                        acgatGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATc                                                                       <  2:266486/140‑1 (MQ=255)                                                        acgatGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATc                                                                       <  2:516633/140‑1 (MQ=255)                                                        acgatGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATc                                                                       <  2:187743/140‑1 (MQ=255)                                                        acgatGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATc                                                                       <  1:337671/140‑1 (MQ=255)                                                        acgatGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATc                                                                       <  1:41677/140‑1 (MQ=255)                                                          gatGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCgg                                                                     <  2:617837/140‑1 (MQ=255)                                                            tGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCgg                                                                     >  1:133306/1‑138 (MQ=255)                                                            tGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCgg                                                                     <  2:133306/138‑1 (MQ=255)                                                            tGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAg                                                                   >  1:738977/1‑140 (MQ=255)                                                            tGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAg                                                                   >  2:762327/1‑140 (MQ=255)                                                              ccACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAgtg                                                                 >  2:153779/1‑140 (MQ=255)                                                               cACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAgtgt                                                                <  1:153779/140‑1 (MQ=255)                                                               cACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAgtgt                                                                <  2:90023/140‑1 (MQ=255)                                                                aCCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTa                                                               <  1:283/140‑1 (MQ=255)                                                                 ccTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAgtgt                                                                <  2:640968/138‑1 (MQ=255)                                                                 ccTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAgtgt                                                                >  1:640968/1‑138 (MQ=255)                                                                 ccTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTaa                                                              >  1:565208/1‑140 (MQ=255)                                                                     tCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAAc                                                            <  1:355374/138‑1 (MQ=255)                                                                     tCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAAc                                                            >  2:355374/1‑138 (MQ=255)                                                                     tCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAAc                                                            >  2:685284/1‑138 (MQ=255)                                                                     tCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAAc                                                            <  1:685284/138‑1 (MQ=255)                                                                                 aaTGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTcc                                              >  1:671300/1‑140 (MQ=255)                                                                                  aTGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCg                                             <  1:123153/140‑1 (MQ=255)                                                                                        ggCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTa                                       >  2:667973/1‑140 (MQ=255)                                                                                            tGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTAATAg                                   <  2:523061/140‑1 (MQ=255)                                                                                              aaaTCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTAATAGCg                                 <  1:762327/140‑1 (MQ=255)                                                                                              aaaTCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTAATAGCg                                 <  2:416315/140‑1 (MQ=255)                                                                                                 tCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTAATAGCGGaa                              <  2:565208/140‑1 (MQ=255)                                                                                                    gTCGGATGGATTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTAATAGCGGAATAg                           >  2:652910/1‑140 (MQ=255)                                                                                                        gatggatTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTAATAGCGGAATAGCCat                       <  2:101252/140‑1 (MQ=255)                                                                                                             atTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTAATAGCGGaa                              <  2:846196/128‑1 (MQ=255)                                                                                                             atTGAGGCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTAATAGCGGaa                              >  1:846196/1‑128 (MQ=255)                                                                                                                   gCCGAGATTGATGAGTGGCTATCACAACGCTGTAGACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTAATAGCGGAATAGCCATATTTGCTAAAc            >  1:477308/1‑140 (MQ=255)                                                                                                                   gCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTAATAGCGGAATAGCCATATTTGCTAAAc            >  1:462582/1‑140 (MQ=255)                                                                                                                   gCCGAGATTGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTAATAGCGGAATAGCCATATTTGCTAAAc            <  2:722199/140‑1 (MQ=255)                                                                                                                          ttGATGAGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTAATAGCGGAATAGCCATATTTGCTAAACAATTTCt     <  2:671300/140‑1 (MQ=255)                                                                                                                             atgaGTGGCTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTAATAGCGGAATAGCCATATTTGCTAAACAATTTCttaa  <  1:667973/140‑1 (MQ=255)                                                                                                                                     |                                                                                                                                    ACAGGTATGGCACGGGCCACCATCTATGACTGGTTGAACCCCAAATCACCACGATACGATGCCACCTTTCCCAAAAAGCGAATGCTCGGCGTGAAATCTGTCGGATGGATTGAGGCCGAGATTGATGAGTGGTTATCACAACGCTGTAAACTTATTTGAGGGTGTTACATGAATTCATACTCAATTGCTGTCATCGGAGTGTAAACATCCTGCTATTTCCGCCATTAATAGCGGAATAGCCATATTTGCTAAACAATTTCTTAA  >  NC_000913/2758698‑2758961

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: ‑