Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,454,909	G→A	pseudogene (93/2646 nt)	yfcU ←	putative outer membrane usher protein YfcU

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,454,909	0	G	A	100.0%	209.5 / NA	59	pseudogene (93/2646 nt)	yfcU	putative outer membrane usher protein YfcU
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (25/34);  total (25/34)

CGCCAATGGCTGTTTATTTAGTTGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCGTCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGAAAAAGAGAATGGTCAGGCATACACGTTTTTATCCGTTTTTATTCTTGTTCGGTCAAAATCC  >  NC_000913/2454774‑2455042                                                                                                                                        |                                                                                                                                      cGCCAATGGCTGTTTATTTAGTTGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCtt                                                                                                                                   >  2:176145/1‑140 (MQ=255)      aTGGCTGTTTATTTAGTTGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCt                                                                                                                                    <  1:662844/134‑1 (MQ=255)      aTGGCTGTTTATTTAGTTGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCt                                                                                                                                    >  2:662844/1‑134 (MQ=255)          cTGTTTATTTAGTTGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGa                                                                                                                          <  1:241399/140‑1 (MQ=255)          cTGTTTATTTAGTTGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGa                                                                                                                          <  1:563188/140‑1 (MQ=255)          cTGTTTATTTAGTTGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGa                                                                                                                          <  1:977215/140‑1 (MQ=255)          cTGTTTATTTAGTTGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGa                                                                                                                          <  1:783940/140‑1 (MQ=255)          cTGTTTATTTAGTTGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGa                                                                                                                          <  2:933434/140‑1 (MQ=255)           tGTTTATTTAGTTGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGac                                                                                                                         <  1:862399/140‑1 (MQ=255)           tGTTTATTTAGTTGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGac                                                                                                                         <  1:451938/140‑1 (MQ=255)            gTTTATTTAGTTGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGaca                                                                                                                        <  2:622021/140‑1 (MQ=255)              ttatttaGTTGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACt                                                                                                                      >  2:464054/1‑140 (MQ=255)                  ttaGTTGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCta                                                                                                                  >  2:716137/1‑140 (MQ=255)                   taGTTGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAACCGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCtat                                                                                                                 <  2:126756/140‑1 (MQ=255)                    aGTTGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCtata                                                                                                                >  2:220648/1‑140 (MQ=255)                     gTTGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATaa                                                                                                               <  1:248972/140‑1 (MQ=255)                      ttGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGccc                                                                                                                             <  1:369646/125‑1 (MQ=255)                      ttGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGccc                                                                                                                             >  2:369646/1‑125 (MQ=255)                       tGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACt                                                                                                             >  1:227393/1‑140 (MQ=255)                       tGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACt                                                                                                             >  2:1106498/1‑140 (MQ=255)                         aaCCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTcc                                                                                                           <  1:172959/140‑1 (MQ=255)                                    tGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGcc                                                                                                >  1:962545/1‑140 (MQ=255)                                        ttttCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAgcg                                                                                            <  1:716137/140‑1 (MQ=255)                                        ttttCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAgcg                                                                                            >  1:466061/1‑140 (MQ=255)                                         tttCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAgcgc                                                                                           >  1:1068366/1‑140 (MQ=255)                                             cGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATg                                                                                       <  1:61240/140‑1 (MQ=255)                                             cGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATg                                                                                       >  1:251677/1‑140 (MQ=255)                                              gggCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGc                                                                                      >  2:1111325/1‑140 (MQ=255)                                               ggCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGca                                                                                     >  1:1009847/1‑140 (MQ=255)                                                gCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGcac                                                                                    >  1:313783/1‑140 (MQ=255)                                                 cTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGcacc                                                                                   <  2:251677/140‑1 (MQ=255)                                                              tggctggAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCg                                                                      >  2:879466/1‑140 (MQ=255)                                                                gctggAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTa                                                                    >  1:1050704/1‑140 (MQ=255)                                                                gctggAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTa                                                                    >  2:1068250/1‑140 (MQ=255)                                                                gctggAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTa                                                                    >  1:613920/1‑140 (MQ=255)                                                                 ctggAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTaa                                                                   <  2:1128891/140‑1 (MQ=255)                                                                 ctggAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTaa                                                                   <  2:613920/140‑1 (MQ=255)                                                                 ctggAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTaa                                                                   <  1:220648/140‑1 (MQ=255)                                                                 ctggAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTaa                                                                   <  1:899966/140‑1 (MQ=255)                                                                     aaaaaCGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGa                                                               >  2:942144/1‑140 (MQ=255)                                                                       aaaCGCTTCAGATCAATTTTTATGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGaaa                                                             <  2:1068366/140‑1 (MQ=255)                                                                        aaCGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGaaaa                                                            <  1:95002/140‑1 (MQ=255)                                                                                  aTCAATTTTTGTGTCGGCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGAAAAAGAGAATGGt                                                  <  2:1091514/140‑1 (MQ=255)                                                                                  aTCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGAAAAAGAGAATGGt                                                  <  1:1111325/140‑1 (MQ=255)                                                                                  aTCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGAAAAAGAGAATGGt                                                  <  1:1106498/140‑1 (MQ=255)                                                                                   tCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGAAAAAGAGAATGGTc                                                 <  2:962029/140‑1 (MQ=255)                                                                                      aTTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGAAAAAGAGAATGGTCAgg                                              <  1:176145/140‑1 (MQ=255)                                                                                           tgtgTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGAAAAAGAGAATGGTCAGGCATac                                         >  2:775954/1‑140 (MQ=255)                                                                                            gtgtCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGAAAAAgaga                                                       <  2:133486/125‑1 (MQ=255)                                                                                            gtgtCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGAAAAAgaga                                                       >  1:133486/1‑125 (MQ=255)                                                                                            gtgtCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGAAAAAGAGAATGGt                                                  >  1:1025923/1‑130 (MQ=255)                                                                                            gtgtCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGAAAAAGAGAATGGt                                                  <  2:1025923/130‑1 (MQ=255)                                                                                                 gCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGAAAAAGAGAATGGTCAGGCATACACGttt                                   >  1:921623/1‑140 (MQ=255)                                                                                                     tttAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGAAAAAGAGAATGGTCAGGCATACACGTTTTTAt                               <  2:15995/140‑1 (MQ=255)                                                                                                      ttAATTCCAGAAAACGGGAATCAAACTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGAAAAAGAGAATGGTCAGGCATACACGTTTTTATc                              <  2:1009847/140‑1 (MQ=255)                                                                                                                            aaaCTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGAAAAAGAGAATGGTCAGGCATACACGTTTTTATCCGTTTTTATTCTTGTTCGGTCa        <  1:665683/140‑1 (MQ=255)                                                                                                                              aCTGAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGAAAAAGAGAATGGTCAGGCATACACGTTTTTATCCGTTTTTATTCTTGTTCGGTCaaa      <  1:758135/140‑1 (MQ=255)                                                                                                                                 gAATGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGAAAAAGAGAATGGTCAGGCATACACGTTTTTATCCGTTTTTATTCTTGTTCGGTCAAAATc   <  1:879466/140‑1 (MQ=255)                                                                                                                                  aaTGTCATCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGAAAAAGAGAATGGTCAGGCATACACGTTTTTATCCGTTTTTATTCTTGTTCGGTCAAAATcc  >  2:151271/1‑140 (MQ=255)                                                                                                                                        |                                                                                                                                      CGCCAATGGCTGTTTATTTAGTTGAACCTGTAAATTGTATTTTCCGGGCTCAACATACCCCTGGCTGGAAAAACGCTTCAGATCAATTTTTGTGTCGCCTTTTAATTCCAGAAAACGGGAATCAAACTGAATGTCGTCTTCAGCCCAGACACTGCTATAACTCCCTGACATTGCCAGCGCAATGCACCACGGAAGAATCCGTAATCGAAAAAGAGAATGGTCAGGCATACACGTTTTTATCCGTTTTTATTCTTGTTCGGTCAAAATCC  >  NC_000913/2454774‑2455042

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑