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%	168.3 / NA	45	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 (18/27);  total (18/27)

CGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTC  >  NC_000913/249881‑250171                                                                                                                                                  |                                                                                                                                                  cGTAGAAATCGGCATCGCTGGCAACAACTTTACGCCGGGTCTGCGCCTGCGCCTGGTTGAGCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATgcgca                                                                                                                                               <  2:137205/150‑2 (MQ=255)  gTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCg                                                                                                                                             <  1:291942/151‑1 (MQ=255)        aTCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCt                                                                                                                                       >  1:299735/1‑151 (MQ=255)          cGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCtt                                                                                                                                      <  1:261817/150‑1 (MQ=255)             ccTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGt                                                                                                                                  <  1:602789/151‑1 (MQ=255)                 gCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTga                                                                                                                                <  2:526261/149‑1 (MQ=255)                 gCTGGCAACATCTTTACGCCGGGTTTGCGACTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTgacg                                                                                                                              >  2:297757/1‑151 (MQ=255)                              ttACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAg                                                                                                                     <  2:67443/147‑1 (MQ=255)                               tACGCCGGGTTTGCGCCTTCGCCTTGTTGATCAATCCGGCGTCACGACCGGCGTCAATCGCCATCTGTTTGCCTGTCATCGCGTCTAAGGTAAAGCGTGTAGACATCTCGGAAATGCGCTCGGCTACGTTGGTGACGCCAATACAGtt                                                                                                                   <  2:230218/148‑1 (MQ=255)                                aCGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGAtt                                                                                                               >  2:75775/1‑151 (MQ=255)                                  gCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGt                                                                                                             <  2:762908/151‑1 (MQ=255)                                   ccGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAAt                                                                                                                         >  1:150497/1‑138 (MQ=255)                                   ccGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAAt                                                                                                                         <  2:150490/138‑1 (MQ=255)                                   ccGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTc                                                                                                            >  1:417150/1‑151 (MQ=255)                                       gTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAAc                                                                                                         >  1:69264/1‑150 (MQ=255)                                         ttGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAg                                                                                                       <  2:342227/150‑1 (MQ=255)                                          tgcgcctgcgccTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGc                                                                                                      <  2:680915/150‑1 (MQ=255)                                           gcgcctgcgcctGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGt                                                                                                    >  2:760640/1‑151 (MQ=255)                                           gcgcctgcgcctGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGt                                                                                                    <  1:133506/151‑1 (MQ=255)                                              cctgcgcctgGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTc                                                                                                   >  1:636780/1‑149 (MQ=255)                                               ctgcgcctgGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGTCATCTGTTTGCCGGGCATCGCGTCTAAGGAAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGCGACGACAATAAAGTTGATTGTCAACAGCGTCAGt                                                                                                >  2:34113/1‑151 (MQ=255)                                                   gcctgGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAAt                                                                                            <  2:750957/151‑1 (MQ=255)                                                       ggTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGa                                                                                        <  1:524586/151‑1 (MQ=255)                                                          tGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGc                                                                                      <  2:360268/150‑1 (MQ=255)                                                              cAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGa                                                                                  <  1:637214/150‑1 (MQ=255)                                                              cAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGa                                                                                  >  1:452775/1‑150 (MQ=255)                                                                      cGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTAt                                                                         <  1:68564/151‑1 (MQ=255)                                                                       gTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATc                                                                        >  1:216517/1‑151 (MQ=255)                                                                          aaGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATcgc                                                                      <  1:131311/150‑1 (MQ=255)                                                                             aTCGGCGTCACTCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCGCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGAGTCAGTAAATCCGAGCGTGAAAGCATTATCGCcgcg                                                                  >  2:11262/1‑151 (MQ=255)                                                                                ggCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTg                                                               <  2:297398/151‑1 (MQ=255)                                                                                  cGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCa                                                             <  1:375766/151‑1 (MQ=255)                                                                                    tCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACg                                                           >  2:447522/1‑151 (MQ=255)                                                                                     cAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACgg                                                          <  2:322081/151‑1 (MQ=255)                                                                                         cGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCa                                                       <  1:235041/150‑1 (MQ=255)                                                                                         cGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAg                                                      <  1:186346/151‑1 (MQ=255)                                                                                             aTCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCg                                                   >  1:618074/1‑150 (MQ=255)                                                                                                 gTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGAt                                                 <  1:504448/148‑1 (MQ=255)                                                                                                            aTCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGgtggtg                                   <  1:434465/151‑1 (MQ=255)                                                                                                            aTCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGgtggtg                                   <  1:629705/151‑1 (MQ=255)                                                                                                                cgTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCt                               >  1:595290/1‑151 (MQ=255)                                                                                                                 gTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTg                              <  2:72452/151‑1 (MQ=255)                                                                                                                      aGGTAAAGCGGGCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGAGTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGcc                         <  2:745992/151‑1 (MQ=255)                                                                                                                               gggCAGAAACCTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTtaaata                 >  1:399398/1‑150 (MQ=255)                                                                                                                                         cTCGGAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCg      >  2:526618/1‑151 (MQ=255)                                                                                                                                             gAAATGCGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGtctc  >  1:207769/1‑151 (MQ=255)                                                                                                                                                  |                                                                                                                                                  CGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATCGCCGCGCTGCACGGGCAGTCGATTTTTAACGGTGGTGGGCTGTCGCCGTTAAATAAAATCAGCCCGTCTC  >  NC_000913/249881‑250171

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑