Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	250,026	A→G	pseudogene (45/1713 nt)	lfhA ←	pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	250,026	0	A	G	100.0%	176.9 / NA	47	pseudogene (45/1713 nt)	lfhA	pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (22/25);  total (22/25)

GCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTC  >  NC_000913/249879‑250171                                                                                                                                                    |                                                                                                                                                  gcCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATgcgc                                                                                                                                                <  2:601893/151‑1 (MQ=255)   cGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTc                                                                                                                                              >  2:923348/1‑151 (MQ=255)       gAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGcc                                                                                                                                          <  1:790092/151‑1 (MQ=255)          aTCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCt                                                                                                                                       >  2:993951/1‑151 (MQ=255)           tCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCtt                                                                                                                                      >  1:1057810/1‑151 (MQ=255)            cGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCtt                                                                                                                                      <  1:641308/150‑1 (MQ=255)                     tGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTgacgac                                                                                                                            >  2:568333/1‑151 (MQ=255)                     tGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTgacgac                                                                                                                            >  1:910419/1‑151 (MQ=255)                      ggCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACa                                                                                                                           <  1:917106/151‑1 (MQ=255)                        cAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAAt                                                                                                                         <  2:725825/151‑1 (MQ=255)                        cAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAAt                                                                                                                         <  1:669175/151‑1 (MQ=255)                          aCATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATaa                                                                                                                       <  1:351019/151‑1 (MQ=255)                               tttACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTg                                                                                                                  >  2:882770/1‑151 (MQ=255)                                   cGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTg                                                                                                              <  1:23979/151‑1 (MQ=255)                                    gCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGt                                                                                                             <  1:134073/151‑1 (MQ=255)                                      cGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTc                                                                                                            >  2:1050354/1‑150 (MQ=255)                                        ggTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAAc                                                                                                         >  1:108885/1‑151 (MQ=255)                                                 ctgcgcctgGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGt                                                                                                >  1:679285/1‑151 (MQ=255)                                                   gcgcctgGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTaa                                                                                              <  1:643586/151‑1 (MQ=255)                                                   gcgcctgGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTaa                                                                                              <  1:349502/151‑1 (MQ=255)                                                   gcgcctgGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTa                                                                                               <  1:279653/150‑1 (MQ=255)                                                    cgcctgGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTaaa                                                                                             <  2:218733/151‑1 (MQ=255)                                                    cgcctgGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTaa                                                                                              >  2:193870/1‑150 (MQ=255)                                                       ctgGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATcc                                                                                          >  1:867676/1‑151 (MQ=255)                                                         ggTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATcc                                                                                          <  2:827532/149‑1 (MQ=255)                                                         ggTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGa                                                                                        <  1:491150/151‑1 (MQ=255)                                                              aTCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTg                                                                                   >  1:701078/1‑151 (MQ=255)                                                                 aaTCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGaa                                                                                 >  2:94394/1‑150 (MQ=255)                                                                      ggCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCAtt                                                                           <  1:718050/151‑1 (MQ=255)                                                                        cGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTAt                                                                         >  1:587419/1‑151 (MQ=255)                                                                               aTCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCcgcg                                                                  >  1:780207/1‑151 (MQ=255)                                                                                  ggCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTg                                                               <  2:870877/151‑1 (MQ=255)                                                                                              cATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCg                                                   >  2:233373/1‑151 (MQ=255)                                                                                                 cTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGAtt                                                >  1:842151/1‑151 (MQ=255)                                                                                                   gTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGa                                                  <  2:1830/147‑1 (MQ=255)                                                                                                     ttGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGAttttt                                             <  1:28481/150‑1 (MQ=255)                                                                                                         cGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACgg                                        <  1:397178/151‑1 (MQ=255)                                                                                                          gggCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACgg                                        >  2:980074/1‑150 (MQ=255)                                                                                                           ggCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACggtg                                      <  1:200936/151‑1 (MQ=255)                                                                                                              aTCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGgtggtg                                   <  2:922603/151‑1 (MQ=255)                                                                                                                        aGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGcc                         >  1:82935/1‑151 (MQ=255)                                                                                                                            aaaGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGtt                      <  1:301322/150‑1 (MQ=255)                                                                                                                                cGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTtaaat                  >  2:1024920/1‑150 (MQ=255)                                                                                                                                 gggCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTtaaataa                <  1:859291/151‑1 (MQ=255)                                                                                                                                 gggCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTtaaataa                <  1:188550/151‑1 (MQ=255)                                                                                                                                     aGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATc            >  1:277104/1‑151 (MQ=255)                                                                                                                                              ggAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGtc    <  2:557166/150‑1 (MQ=255)                                                                                                                                                aaaTGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGtctc  >  2:170579/1‑150 (MQ=255)                                                                                                                                                    |                                                                                                                                                  GCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTC  >  NC_000913/249879‑250171

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑