Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	250,190	C→T	pseudogene (119/756 nt)	lafU →	flagellar system protein, promoterless fragment

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	250,190	0	C	T	100.0%	171.0 / NA	49	pseudogene (119/756 nt)	lafU	flagellar system protein, promoterless fragment
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (25/24);  total (25/24)

TGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCACCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGATG  >  NC_000913/250062‑250318                                                                                                                                 |                                                                                                                                 tGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGc                                                                                                                       >  2:502389/1‑140 (MQ=255)          cGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGc                                                                                                                            <  2:504698/126‑1 (MQ=255)          cGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGc                                                                                                                            >  1:504698/1‑126 (MQ=255)          cGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAgaga                                                                                                              >  1:256351/1‑140 (MQ=255)          cGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAgaga                                                                                                              >  2:165333/1‑140 (MQ=255)            tCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACg                                                                                                            >  1:461177/1‑140 (MQ=255)             cAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGGCGGAAGAGACgg                                                                                                           >  2:762434/1‑140 (MQ=255)              aGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACggg                                                                                                          >  1:417175/1‑139 (MQ=255)                        aGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAgcg                                                                                                >  1:224535/1‑140 (MQ=255)                          cGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGcgcg                                                                                              <  2:519513/140‑1 (MQ=255)                            tGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTg                                                                                            <  2:417175/140‑1 (MQ=255)                               aaGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGAtg                                                                                         <  2:256351/140‑1 (MQ=255)                                       tCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATgag                                                                                 >  1:844571/1‑140 (MQ=255)                                       tCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATgag                                                                                 >  1:844570/1‑140 (MQ=255)                                              gcTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATATGAATGAGAAAACgg                                                                          <  1:750292/140‑1 (MQ=255)                                               cTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGaa                                                                                     <  2:481748/128‑1 (MQ=255)                                               cTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGaa                                                                                     >  1:481748/1‑128 (MQ=255)                                                      ggCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGctgctg                                                                  <  2:224535/140‑1 (MQ=255)                                                         aGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTgaag                                                               >  1:357459/1‑140 (MQ=255)                                                            cGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTgaagaag                                                            >  2:538776/1‑140 (MQ=255)                                                                   tAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGctgctg                                                                  >  1:537841/1‑127 (MQ=255)                                                                   tAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGctgctg                                                                  <  2:537841/127‑1 (MQ=255)                                                                       ggtggtGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAACCCGCCAc                                                 <  2:461177/140‑1 (MQ=255)                                                                         tggtggGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCg                                               >  1:355305/1‑140 (MQ=255)                                                                         tggtggGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTACCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCg                                               >  2:727583/1‑140 (MQ=255)                                                                          ggtggGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGa                                              <  2:851644/140‑1 (MQ=255)                                                                           gtggGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGGGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAg                                             >  2:352545/1‑140 (MQ=255)                                                                                   tCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTTGCGGGAGAGACGGAGCAAAAAAGGCGTGGTGTGAATGAGAAAACGGCGCTGCTGAAGAAAAAATCCGCCCCCGAGCTTGGGGa                                     >  2:782068/1‑140 (MQ=255)                                                                                   tCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGa                                     >  1:571042/1‑140 (MQ=255)                                                                                   tCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGa                                     >  2:6391/1‑140 (MQ=255)                                                                                   tCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGa                                     >  1:675234/1‑140 (MQ=255)                                                                                            aataaaATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAAc                            <  1:488992/140‑1 (MQ=255)                                                                                             ataaaATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAAcc                           <  2:954835/140‑1 (MQ=255)                                                                                             ataaaATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAAcc                           <  1:502389/140‑1 (MQ=255)                                                                                             ataaaATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAAcc                           <  1:418898/140‑1 (MQ=255)                                                                                             ataaaATCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTACCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAAcc                           <  1:727583/140‑1 (MQ=255)                                                                                                  aTCAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTAt                      <  1:762434/140‑1 (MQ=255)                                                                                                    cAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCa                    <  1:724009/140‑1 (MQ=255)                                                                                                    cAGCCCGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCa                    <  2:249978/140‑1 (MQ=255)                                                                                                       cccGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCa                          <  2:464984/131‑1 (MQ=255)                                                                                                       cccGTCTCATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCa                          >  1:464984/1‑131 (MQ=255)                                                                                                           tctcATCCGCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCAt             >  2:198685/1‑140 (MQ=255)                                                                                                                   gCCAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTg     <  1:381780/140‑1 (MQ=255)                                                                                                                     cAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGAt   >  1:895131/1‑140 (MQ=255)                                                                                                                     cAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGAt   >  1:786128/1‑140 (MQ=255)                                                                                                                     cAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGAt   <  1:352545/140‑1 (MQ=255)                                                                                                                     cAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGAt   <  2:786128/140‑1 (MQ=255)                                                                                                                     cAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGAt   <  1:538776/140‑1 (MQ=255)                                                                                                                     cAAAACCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGAt   <  2:895131/140‑1 (MQ=255)                                                                                                                      aaaaCCTGCCATCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGATg  >  1:1002216/1‑140 (MQ=255)                                                                                                                                 |                                                                                                                                 TGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTCATCCGCCAAAACCTGCCACCGTGGCGGTGCCGGAAGAGACGGAGAAAAAAGCGCGTGATGTGAATGAGAAAACGGCGCTGCTGAAGAAGAAATCCGCCACCGAGCTTGGTGAGCTGGCAACCAGTATCAACACCATTGCCCGTGATG  >  NC_000913/250062‑250318

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑