Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,595,669	A→G	pseudogene (2418/5422 nt)	yneO ←	AIDA‑I family autotransporter YneO

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,595,669	0	A	G	100.0%	200.8 / NA	57	pseudogene (2418/5422 nt)	yneO	AIDA‑I family autotransporter YneO
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (26/31);  total (26/31)

ATGGTACCTCCATTCATGGCCAGTCCACCAATGGATTGCTCTCCAACTTTTACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTACTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATCAAGCCATCGCCTTTGAGCGCATTGGTCAGCGTGTAATCTC  >  NC_000913/1595538‑1595802                                                                                                                                    |                                                                                                                                      atgGTACCTCCATTCATGGCCAGTCCACCAATGGATTGCTCTCCAACTTTTACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCttt                                                                                                                               <  2:2867/140‑1 (MQ=255) atgGTACCTCCATTCATGGCCAGTCCACCAATGGATTGCTCTCCAACTTTTACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCttt                                                                                                                               <  1:580964/140‑1 (MQ=255)    gTACCTCCATTCATGGCCAGTCCACCAATGGATTGCTCTCCAACTTTTACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAg                                                                                                                            <  2:171203/140‑1 (MQ=255)              tCATGGCCAGTCCACCAATGGATTGCTCTCCAACTTTTACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAaca                                                                                                                  <  1:642170/140‑1 (MQ=255)                  ggCCAGTCCACCAATGGATTGCTCTCCAACTTTTACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGATGTCGCGTACCAGAGTTAAGGTGCTGTCTTGCAGTTGGGCAACACCgg                                                                                                              >  2:233689/1‑140 (MQ=255)                       gTCCACCAATGGATTGCTCTCCAACTTTTACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAAt                                                                                                         <  2:477027/140‑1 (MQ=255)                        tCCACCAATGGATTGCTCTCCAACTTTTACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAAtt                                                                                                        >  2:15259/1‑140 (MQ=255)                        tCCACCAATGGATTGCTCTCCAACTTTTACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAAtt                                                                                                        >  1:745159/1‑140 (MQ=255)                        tCCACCAATGGATTGCTCTCCAACTTTTACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAAtt                                                                                                        >  2:665771/1‑140 (MQ=255)                        tCCACCAATGGATTGCTCTCCAACTTTTACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAAtt                                                                                                        >  1:632689/1‑140 (MQ=255)                        gccaccaATGGATTGCTCTCCAGCTTTTACCGATGTGTTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAAtt                                                                                                        <  1:374973/139‑1 (MQ=255)                                  gATTGCTCTCCAACTTTTACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGt                                                                                                    <  2:535614/134‑1 (MQ=255)                                  gATTGCTCTCCAACTTTTACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGt                                                                                                    >  1:535614/1‑134 (MQ=255)                                  gATTGCTCTCCAACTTTTACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGt                                                                                              >  2:714176/1‑140 (MQ=255)                                  gATTGCTCTCCAACTTTTACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGACTTTCAGTTGGACAGCACCGGCGAATTCAGTCCCTGt                                                                                              >  1:385057/1‑140 (MQ=255)                                    ttGCTCTCCAACTTTTACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGCAGGTGCTGTCTTACAGGTGGGCAACACCGGCGAATTCAGTCCCTGTTg                                                                                            >  2:222306/1‑140 (MQ=255)                                    ttGCTCTCCAACTTTTACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTg                                                                                            >  2:679194/1‑140 (MQ=255)                                      gCTCTCCAACTTTTACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCa                                                                                          <  2:484166/140‑1 (MQ=255)                                       ctctCCAACTTTTACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCAt                                                                                         >  1:425683/1‑140 (MQ=255)                                            cAACTTTTCCCGATGTGGTATTCTCACTGTCAGACTGCACCATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTa                                                                                    <  2:385057/140‑1 (MQ=255)                                                  ttACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGcc                                                                               >  1:583045/1‑139 (MQ=255)                                                  ttACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGcc                                                                               <  2:583045/139‑1 (MQ=255)                                                  ttACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGcc                                                                               >  1:156439/1‑139 (MQ=255)                                                  ttACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGcc                                                                               <  2:156439/139‑1 (MQ=255)                                                  ttACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCa                                                                              <  2:514428/140‑1 (MQ=255)                                                  ttACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCa                                                                              >  1:458760/1‑140 (MQ=255)                                                         tgtgGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACAt                                                                         <  2:816429/138‑1 (MQ=255)                                                         tgtgGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACAt                                                                         >  1:816429/1‑138 (MQ=255)                                                             gTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTc                                                                   >  2:796891/1‑140 (MQ=255)                                                                     aCTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATg                                                           >  1:143281/1‑140 (MQ=255)                                                                              cTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCa                                                  <  1:665771/140‑1 (MQ=255)                                                                               tGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCAc                                                 <  2:425683/140‑1 (MQ=255)                                                                                gCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACt                                                <  2:184384/140‑1 (MQ=255)                                                                                gCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACt                                                <  2:514216/140‑1 (MQ=255)                                                                                 cAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTc                                               >  1:568583/1‑140 (MQ=255)                                                                                   aCATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGCAGGATGACAGCTGCACTCGc                                             >  2:71438/1‑140 (MQ=255)                                                                                      tCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATc                                          <  2:423770/140‑1 (MQ=255)                                                                                      tCGCGTGAGTAAGCGAAGCGGTCTTCTCGCGTTCCAGCGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATc                                          <  1:233689/140‑1 (MQ=255)                                                                                       cgcgTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATCa                                         >  1:760134/1‑140 (MQ=255)                                                                                       cgcgTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATCa                                         >  1:559076/1‑140 (MQ=255)                                                                                       cgcgTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCAAGGGTAAAGCCAAACATTTTGTCGGACGATGATAGCTGCACTCGCATCa                                         >  2:356619/1‑140 (MQ=255)                                                                                         cgTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATCAAg                                       >  2:483220/1‑140 (MQ=255)                                                                                            gAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATCAAGCCa                                    <  1:661080/140‑1 (MQ=255)                                                                                            gAGTAAGCGCAGCGGTGATGTCGCGTTCCAGTGTGTAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATCAAGCCa                                    <  2:249631/140‑1 (MQ=255)                                                                                             aGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATCAAGCCAt                                   <  2:143281/140‑1 (MQ=255)                                                                                                    gcAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGAAAGCAGCACTCGCAGCAAGCCATCGCCttt                            >  1:389276/1‑140 (MQ=255)                                                                                                      aGCGGTGTTGTCGCGTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATCAAGCCATCGCCTTTGa                          <  2:632689/140‑1 (MQ=255)                                                                                                                  gcgTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATCAAGCCATCGCCTTTGAGCGCATTGGTCa              >  2:782236/1‑140 (MQ=255)                                                                                                                    gTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATCAAGCCATCGCCTTTGAGTGCATTGGTCAGc            <  1:15259/140‑1 (MQ=255)                                                                                                                    gTTCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATCAAGCCATCGCCTTTGAGCGCATTGGTCAGc            <  2:198184/140‑1 (MQ=255)                                                                                                                     ttCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATCAAGCCATCGCCTTTGAGCGCATTGGTCa              >  1:740318/1‑137 (MQ=255)                                                                                                                     ttCCAGAGTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATCAAGCCATCGCCTTTGAGCGCATTGGTCa              <  2:740318/137‑1 (MQ=255)                                                                                                                         agagTGAAGGTGCTGTTCTTCACTTGGGCAACATCGGCGGATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATCAAGCCATCGCCTTTGAGCGCATTGGTCAGCGTGTa       <  2:389276/140‑1 (MQ=255)                                                                                                                         agagTGAAGGTGCTGTCTTTCATTTTGGCAACACCGGAGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATCAAGCCATCGCCTTTGAGCGCATTGGTCAGCGTGTa       <  1:356619/140‑1 (MQ=255)                                                                                                                         agagTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATCAAGCCATCGCCTTTGAGCGCATTGGTCAGCGTGTa       <  1:525069/140‑1 (MQ=255)                                                                                                                         agagTGAAGGTGCTGCCTTTCACTTCGGCAACACCGGTGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATCAAGCCATCGCCTTTGAGCGCATTGGTCAGCGTGTa       <  1:249176/140‑1 (MQ=255)                                                                                                                           agTGAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATCAAGCCATCGCCTTTGAGCGCATTGGTCAGCGTGTAAt     <  1:782236/140‑1 (MQ=255)                                                                                                                              gAAGGTGCTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATCAAGCCATCGCCTTTGAGCGCATTGGTCAGCGTGTAAtctc  <  2:568583/140‑1 (MQ=255)                                                                                                                                    |                                                                                                                                      ATGGTACCTCCATTCATGGCCAGTCCACCAATGGATTGCTCTCCAACTTTTACCGATGTGGTATTTTCACTGTCAGACTGCAACATCGCGTGAGTAAGCGCAGCGGTGTTGTCGCGTTCCAGAGTGAAGGTACTGTCTTTCAGTTGGGCAACACCGGCGAATTCAGTCCCTGTTGCATGGGTAAAGCCAAACATCTTGTCGGAGGATGACAGCTGCACTCGCATCAAGCCATCGCCTTTGAGCGCATTGGTCAGCGTGTAATCTC  >  NC_000913/1595538‑1595802

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑