Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,471,105	G→A	pseudogene (291/291 nt) P138L (CCT→CTT)	tfaS → yfdK ←	pseudogene, CPS‑53 (KpLE1) prophage, tail fiber assembly protein fragment,Phage or Prophage Related CPS‑53 (KpLE1) prophage, conserved protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,471,105	0	G	A	100.0%	172.6 / NA	54	pseudogene (291/291 nt) P138L (CCT→CTT)	tfaS yfdK	pseudogene, CPS‑53 (KpLE1) prophage, tail fiber assembly protein fragment,Phage or Prophage Related CPS‑53 (KpLE1) prophage, conserved protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (24/30);  total (24/30)

ATTACAGGCTGGGCGGAAGCTGATGCAGGCAGAGACCTCCCGACTTAACACTGTGCTGGATTACATTGACGCGGTGACGGCAACAGATACCAGCACCGCGCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAGGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCTCACCTTTCAGACGACCAATAGCCGCTTTACCAGCCCATTGTTTACTGT  >  NC_000913/2470970‑2471240                                                                                                                                        |                                                                                                                                        aTTACAGGCTGGGCGGAAGCTGATGCAGGCAGAGACCTCCCGACTTAACACTGTGCTGGATTACATTGACGCGGTGACGGCAACAGATACCAGCACCGCGCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGcc                                                                                                                                      <  1:665449/139‑1 (MQ=255)             gCGGAAGCTGATGCAGGCAGAGACCTCCCGACTTAACACTGTGCTGGATTACATTGACGCGGTGACGGCAACAGATACCAGCACCGCGCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTg                                                                                                                          >  2:814788/1‑139 (MQ=255)              cGGAAGCTGATGCAGGCAGAGACCTCCCGACTTAACACTGTGCTGGATTACATTGACGCGGTGACGGCAACAGATACCAGCACCGCGCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTgg                                                                                                                         <  2:17807/139‑1 (MQ=255)              cGGAAGCTGATGCAGGCAGAGACCTCCCGACTTAACACTGTGCTGGACTACATTGACGCGGTGACGGCAACAGATACCAGCACCGCGCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTgg                                                                                                                         <  1:854462/139‑1 (MQ=255)                       aTGCAGGCAGAGACCTCCCGACTTAACACTGTGCTGGATTACATTGACGCGGTGACGGCAACAGATACCAGCACCGCGCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGa                                                                                                                >  2:1328461/1‑139 (MQ=255)                                gagaCCTCCCGACTTAACACTGTGCTGGATTACATTGACGCGGTGACGGCAACAGATACCAGCACCGCGCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGAc                                                                                                       <  1:551480/139‑1 (MQ=255)                                                      tgCTGGATTACATTGACGCGGTGACGGCAACAGATACCAGCACCGCGCCGGTTGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGAc                                                                                                       >  1:1065823/1‑117 (MQ=255)                                                      tgCTGGATTACATTGACGCGGTGACGGCAACAGATACCAGCACCGCGCCGGTTGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGAc                                                                                                       <  2:1065823/117‑1 (MQ=255)                                                      tgCTGGATTACATTGACGCGGTGACGGCAACAGATACCAGCACCGCGCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGAc                                                                                                       >  2:1191102/1‑117 (MQ=255)                                                      tgCTGGATTACATTGACGCGGTGACGGCAACAGATACCAGCACCGCGCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGAc                                                                                                       <  1:1191102/117‑1 (MQ=255)                                                        cTGGATTACATTGACGCGGTGACGGCAACAGATACCAGCACCGCGCCGGATGTCATCTGGCCTTAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATc                                                                               >  2:468931/1‑139 (MQ=255)                                                           gATTACATTGACGCGGTGACGGCAACAGATACCAGCACCGCGCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCTAtt                                                                                                                                   <  2:533545/84‑1 (MQ=255)                                                           gATTACATTGACGCGGTGACGGCAACAGATACCAGCACCGCGCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCAtt                                                                                                                                   >  1:533545/1‑84 (MQ=18)                                                              tACATTGACGCGGTGACGGCAACAGATACCAGCACCGCGCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCca                                                                         <  1:814788/139‑1 (MQ=255)                                                               aCATTGACGCGGTGACGGCAACAGATACCAGCACCGCGCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCcac                                                                        <  1:459946/139‑1 (MQ=255)                                                                  ttGACGCGGTGACGGCAACAGATACCAGCACCGCGCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGgcg                                                                                                                       >  2:75637/1‑89 (MQ=18)                                                                  ttGACGCGGTGACGGCAACAGATACCAGCACCGCGCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGgcg                                                                                                                       <  1:75637/89‑1 (MQ=25)                                                                                     aGATACCAGCACCGCGCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGGCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCt                                                  <  2:683486/139‑1 (MQ=255)                                                                                       aTACCAGCACCGCGCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGt                                                                                             <  2:714040/94‑1 (MQ=255)                                                                                       aTACCAGCACCGCGCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGt                                                                                             >  1:714040/1‑94 (MQ=255)                                                                                              cACCGCGCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCTCACCTTTCa                                         >  2:1362327/1‑139 (MQ=255)                                                                                                 cgcgCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTAt                                                                                                           >  1:965260/1‑70 (MQ=255)                                                                                                 cgcgCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTAt                                                                                                           <  2:965260/70‑1 (MQ=255)                                                                                                  gcgcCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCTCACCTTTCAgacg                                     >  2:1143115/1‑139 (MQ=255)                                                                                                   cgcCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGgcg                                                                                                                       >  1:565292/1‑56 (MQ=255)                                                                                                   cgcCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGgcg                                                                                                                       <  2:565292/56‑1 (MQ=255)                                                                                                   cgcCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGAc                                                                                                       >  1:1254153/1‑72 (MQ=255)                                                                                                   cgcCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGAc                                                                                                       >  2:187069/1‑72 (MQ=255)                                                                                                   cgcCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGAc                                                                                                       <  1:187069/72‑1 (MQ=255)                                                                                                   cgcCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGAc                                                                                                       <  2:1254153/72‑1 (MQ=255)                                                                                                   cgcCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGt                                                                                         >  1:1036503/1‑86 (MQ=255)                                                                                                   cgcCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGt                                                                                         <  2:1036503/86‑1 (MQ=255)                                                                                                   cgcCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCTCACCTTTCAgacga                                    >  1:404067/1‑139 (MQ=255)                                                                                                   cgcCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCTCACCTTTCAga                                       >  1:74657/1‑136 (MQ=255)                                                                                                   cgcCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCTCACCTTTCAga                                       <  2:74657/136‑1 (MQ=255)                                                                                                         aTGTCATCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCTCACCTTTCAGACGACCAATa                              <  2:310131/139‑1 (MQ=255)                                                                                                              aTCTGGCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCTCACCTTTCAGACGACCAATAGCCGc                         <  2:758711/139‑1 (MQ=255)                                                                                                                   gCCTTAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCTCACCTTTCAGACGACCAATAGCCGCTTTAc                    <  1:468931/139‑1 (MQ=255)                                                                                                                   gCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGAc                                                                                                       >  1:568629/1‑56 (MQ=255)                                                                                                                   gCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGAc                                                                                                       <  2:568629/56‑1 (MQ=255)                                                                                                                   gCCTGAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCTCACCTTTCAGACGACCAATAGCCGCTTTAc                    <  1:1362327/139‑1 (MQ=255)                                                                                                                       gAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCTCACCTTTCAGACGACCAATa                              <  1:1136653/125‑1 (MQ=255)                                                                                                                       gAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCTCACCTTTCAGACGACCAATa                              >  2:1136653/1‑125 (MQ=255)                                                                                                                       gAACTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCTCACCTTTCAGACGACCAATAGCCGCTTTACCAGc                <  2:404067/139‑1 (MQ=255)                                                                                                                        aaCTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCTCACCTTTCAGACGACCAATAGCCGCTTTACCAGcc               >  1:1343726/1‑139 (MQ=255)                                                                                                                          cTGCCGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCTCACCTTTCAGACGACCAATAGCCGCTTTACCAGCCCa             <  2:498320/139‑1 (MQ=255)                                                                                                                             ccGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGcc                                                                          <  2:210115/75‑1 (MQ=255)                                                                                                                             ccGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGcc                                                                          >  1:210115/1‑75 (MQ=255)                                                                                                                             ccGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCTCACCTTTCAGACGACCAATAGCCGCTTTACCAGCCCATTg          >  1:1364310/1‑139 (MQ=255)                                                                                                                             ccGGAGGAGTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCTCACCTTTCAGACGACCAATAGCCGCTTTACCAGCCCATTg          >  1:1127351/1‑139 (MQ=255)                                                                                                                                   gagTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAg                                                                                              <  1:122245/49‑1 (MQ=255)                                                                                                                                   gagTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAg                                                                                              >  2:122245/1‑49 (MQ=255)                                                                                                                                   gagTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCTCACCTTTCAGACGACCAATAGCCGCTTTACCAGCCCATTGTTTACt    <  2:1364310/139‑1 (MQ=255)                                                                                                                                     gTAAGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCTCACCTTTCAGACGACCAATAGCCGCTTTACCAGCCCATTGTTTACTGt  <  1:235717/139‑1 (MQ=255)                                                                                                                                        |                                                                                                                                        ATTACAGGCTGGGCGGAAGCTGATGCAGGCAGAGACCTCCCGACTTAACACTGTGCTGGATTACATTGACGCGGTGACGGCAACAGATACCAGCACCGCGCCGGATGTCATCTGGCCTGAACTGCCGGAGGAGTAGGCCATTCAATATCTGGCGCACTGGAAGTATCGACCAGCTCCAGTGCGTCCAGATAATCCAGCCACAAATTATATTGCGCCAGTTCCTCACCTTTCAGACGACCAATAGCCGCTTTACCAGCCCATTGTTTACTGT  >  NC_000913/2470970‑2471240

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑