Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,778,122	A→C	intergenic (+340/+24)	ypjF → / ← ypjA	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,778,122	0	A	C	100.0%	169.3 / NA	46	intergenic (+340/+24)	ypjF/ypjA	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (25/21);  total (25/21)

CCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACAGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATACCCCACCCCAAGATGCCCGCTTAACGTACTGCTGAATGAGGCTTTAATACCTGCCT  >  NC_000913/2777979‑2778267                                                                                                                                                |                                                                                                                                                  cccACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTgg                                                                                                                                            <  1:417752/151‑1 (MQ=255)          cATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTc                                                                                                                                    <  1:644789/150‑1 (MQ=255)             gATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGtt                                                                                                                                 <  2:105480/150‑1 (MQ=255)              aTTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTg                                                                                                                                >  2:314023/1‑150 (MQ=255)                     ggTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTc                                                                                                                          >  1:286304/1‑149 (MQ=255)                          aaGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGa                                                                                                                   <  1:887100/151‑1 (MQ=255)                                 acacCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTATTTCGTTGATGGTCAGAACGACCAGTTc                                                                                                            >  1:211195/1‑151 (MQ=255)                                     caacaaAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCacac                                                                                                        <  1:872731/151‑1 (MQ=255)                                      aacaaAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACAcc                                                                                                       <  2:647441/151‑1 (MQ=255)                                          aaaaCAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCt                                                                                                   <  2:446799/151‑1 (MQ=255)                                          aaaaCAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCt                                                                                                   >  1:741610/1‑151 (MQ=255)                                           aaaCAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGc                                                                                                    >  2:313157/1‑149 (MQ=255)                                            aaCAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTAc                                                                                                 <  2:870254/151‑1 (MQ=255)                                            aaCAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTAc                                                                                                 >  2:225634/1‑151 (MQ=255)                                                 gAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGt                                                                                            <  2:280375/151‑1 (MQ=255)                                                      tAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCAc                                                                                       >  1:454775/1‑151 (MQ=255)                                                         aaGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACggg                                                                                    >  2:500732/1‑151 (MQ=255)                                                               cAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGAt                                                                                 <  2:28412/148‑1 (MQ=255)                                                                   aaaaCACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCacac                                                                          >  2:329194/1‑151 (MQ=255)                                                                      acgccGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCcacctcg                                                                        <  2:807734/147‑5 (MQ=255)                                                                          cGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACt                                                                   >  2:405370/1‑151 (MQ=255)                                                                          cGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACt                                                                   >  2:187037/1‑151 (MQ=255)                                                                             ccAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATg                                                                <  2:775259/151‑1 (MQ=255)                                                                              cAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATgg                                                               >  1:146671/1‑151 (MQ=255)                                                                                   ggTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCtat                                                           >  1:862218/1‑150 (MQ=255)                                                                                    gTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATac                                                         <  2:328977/151‑1 (MQ=255)                                                                                             cATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATaccccacccc                                                 >  1:226818/1‑150 (MQ=255)                                                                                              aTAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATAccccacccca                                                >  1:254164/1‑150 (MQ=255)                                                                                                           cAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATACCCCACCCCAAGATGCCCGCTTa                                   >  2:649113/1‑150 (MQ=255)                                                                                                            aaaGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATACCCCACCCCAAGATGCCCGCTTAAc                                 >  2:887824/1‑151 (MQ=255)                                                                                                            aaaGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATACCCCACCCCAAGATGCCCGCTTAAc                                 >  2:695032/1‑151 (MQ=255)                                                                                                                   ccGCGGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATACCCCACCCCAAGATGCCCGCTTAACGTActgc                          <  2:454763/151‑1 (MQ=255)                                                                                                                    cgcgGCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATACCCCACCCCAAGATGCCCGCTTAACGTActgct                         <  1:585120/151‑1 (MQ=255)                                                                                                                        gCTCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATACCCCACCCCAAGATGCCCGCTTAACGTACTGCTGAAt                     >  2:738711/1‑151 (MQ=255)                                                                                                                          tCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATACCCCACCCCAAGATGCCCGCTTAACGTACTGCTGAATg                    >  2:107903/1‑150 (MQ=255)                                                                                                                          tCCTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATACCCCACCCCAAGATGCCCGCTTAACGTACTGCTGAATg                    >  1:12632/1‑150 (MQ=255)                                                                                                                           ccTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATACCCCACCCCAAGATGCCCGCTTAACGTACTGCTGAATg                    <  2:304678/149‑1 (MQ=255)                                                                                                                           ccTGGTAACATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATACCCCACCCCAAGATGCCCGCTTAACGTACTGCTGAATg                    >  2:869738/1‑149 (MQ=255)                                                                                                                                  aCATGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATACCCCACCCCAAGATGCCCGCTTAACGTACTGCTGAATGAGGCTTTaa           <  1:874152/151‑1 (MQ=255)                                                                                                                                     tGAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATACCCCACCCCAAGATGCCCGCTTAACGTACTGCTGAATGAGGCTTTAATAc        >  1:444675/1‑151 (MQ=255)                                                                                                                                      gAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATACCCCACCCCAAGATGCCCGCTTAACGTACTGCTGAATGAGGCTTTAATAcc       <  1:307143/151‑1 (MQ=255)                                                                                                                                      gAAAGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATACCCCACCCCAAGATGCCCGCTTAACGTACTGCTGAATGAGGCTTTAATAcc       >  2:25694/1‑151 (MQ=255)                                                                                                                                       aaaGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATACCCCACCCCAAGATGCCCGCTTAACGTACTGCTGAATGAGGCTTTAATAcct      <  1:459337/151‑1 (MQ=255)                                                                                                                                         aGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATACCCCACCCCAAGATGCCCGCTTAACGTACTGCTGAATGAGGCTTTAATAcctgc    >  1:601308/1‑151 (MQ=255)                                                                                                                                         aGCCCACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATACCCCACCCCAAGATGCCCGCTTAACGTACTGCTGAATGAGGCTTTAATAcctgc    <  2:816960/151‑1 (MQ=255)                                                                                                                                           cccACCGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATACCCCACCCCAAGATGCCCGCTTAACGTACTGCTGAATGAGGCTTTAATAcctgcct  <  1:551502/151‑1 (MQ=255)                                                                                                                                                |                                                                                                                                                  CCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACAGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTATGGCTATACCCCACCCCAAGATGCCCGCTTAACGTACTGCTGAATGAGGCTTTAATACCTGCCT  >  NC_000913/2777979‑2778267

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑