Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	249,034	G→A	pseudogene (1037/1713 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	249,034	0	G	A	100.0%	192.0 / NA	52	pseudogene (1037/1713 nt)	lfhA	pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (38/14);  total (38/14)

CGGTGCCGTCGACGATAAACGGTTATGCAACTGCGTAATATCATCATAGTTAAACAAATCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCGCCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGGGCAGGGCCATCAGTTTATCCGCCGGAATATCCGCTTCATCAGCCTTT  >  NC_000913/248892‑249180                                                                                                                                               |                                                                                                                                                   cgGTGCCGTCGACGATAAACGGTTATGCAACTGCGTAATATCATCATAGTTAAACAAATCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCt                                                                                                                                            <  1:101401/151‑1 (MQ=255)           gacgaTAAACGGTTATGCAACTGCGTAATATCATCATAGTTAAACAAATCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGcgccg                                                                                                                                  >  1:530450/1‑151 (MQ=255)            acgaTAAACGGTTATGCAACTGCGTAATATCATCATAGTTAAACAAATCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGcgccgc                                                                                                                                 >  2:651490/1‑151 (MQ=255)            acgaTAAACGGTTATGCAACTGCGTAATATCATCATAGTTAAACAAATCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGcgccgc                                                                                                                                 >  2:591902/1‑151 (MQ=255)                tAAACGGTTATGCAACTGCGTAATATCATCATAGTTAAACAAATCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTgg                                                                                                                             >  2:651293/1‑151 (MQ=255)                  aaCGGTTATGCAACTGCGTAATATCATCATAGTTAAACAAATCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGAt                                                                                                                           >  2:289022/1‑151 (MQ=255)                     ggTTATGCAACTGCGTAATATCATCATAGTTAAACAAATCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATcc                                                                                                                         >  2:400894/1‑150 (MQ=255)                     ggTTATGCAACTGCGTAATATCATCATAGTTAAACAAATCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCa                                                                                                                        <  2:180891/151‑1 (MQ=255)                         aTGCAACTGCGTAATATCATCATAGTTAAACAAATCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGt                                                                                                                     <  2:642601/150‑1 (MQ=255)                         aTGCAACTGCGTAATATCATCATAGTTAAACAAATCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTg                                                                                                                    >  2:201167/1‑151 (MQ=255)                           gCAACTGCGTAATATCATCATAGTTAAACAAATCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGAc                                                                                                                  >  1:567868/1‑151 (MQ=255)                             aaCTGCGTAATATCATCATAGTTAAACAAATCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCg                                                                                                                <  1:469880/151‑1 (MQ=255)                                 gCGTAATATCATCATAGTTAAACAAATCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCAt                                                                                                            >  2:450296/1‑151 (MQ=255)                                    tAATATCATCATAGTTAAACAAATCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCGGCCTGGATCCAGGTGACCGGCATccc                                                                                                         >  1:547860/1‑151 (MQ=255)                                       tatCATCATAGTTAAACAAATCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGt                                                                                                       >  2:412173/1‑150 (MQ=255)                                        atcatcATAGTTAAACAAATCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTAc                                                                                                     >  2:592503/1‑151 (MQ=255)                                           atcatAGTTAAACAAATCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGcc                                                                                                  >  2:213348/1‑151 (MQ=255)                                                         aaTCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTg                                                                                    >  2:446852/1‑151 (MQ=255)                                                           tCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGc                                                                                   >  1:536557/1‑150 (MQ=255)                                                               gAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGcc                                                                              <  1:141757/151‑1 (MQ=255)                                                                   ataGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTc                                                                           >  1:378885/1‑150 (MQ=255)                                                                        tGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAAtctc                                                                     >  2:451862/1‑151 (MQ=255)                                                                              caATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGt                                                                >  1:134256/1‑150 (MQ=255)                                                                                aTCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAgg                                                             >  1:534012/1‑151 (MQ=255)                                                                                aTCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAgg                                                             >  1:277261/1‑151 (MQ=255)                                                                                aTCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAgg                                                             >  2:338334/1‑151 (MQ=255)                                                                                  cTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGtt                                                           >  2:416108/1‑151 (MQ=255)                                                                                   ttATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGttt                                                          >  2:496135/1‑151 (MQ=255)                                                                                       ttACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCt                                                      >  1:651339/1‑151 (MQ=255)                                                                                           aTGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTgg                                                    >  1:139007/1‑149 (MQ=255)                                                                                             gggTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGagg                                                 <  1:392930/150‑1 (MQ=255)                                                                                                tAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGagggc                                               >  2:436998/1‑149 (MQ=255)                                                                                                 aGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGagggcagg                                            <  2:364538/151‑1 (MQ=255)                                                                                                      tCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGGGCAGGGCCAt                                       >  2:392465/1‑151 (MQ=255)                                                                                                        aCGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGGGCAGGGCCATc                                      >  1:466521/1‑150 (MQ=255)                                                                                                        aCGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGGGCAGGGCCATc                                      >  1:209990/1‑150 (MQ=255)                                                                                                         cGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGGGCAGGGCCATc                                      >  2:675650/1‑149 (MQ=255)                                                                                                             ggCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGGGCAGGGCCATCAGttt                                 >  2:550833/1‑150 (MQ=255)                                                                                                             ggCGCTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGCGCAGGGCCATCAGttt                                 <  1:17910/150‑1 (MQ=255)                                                                                                                gcTGTCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGGGCAGGGCCATCAGTTTATcc                             <  1:560116/151‑1 (MQ=255)                                                                                                                    tCGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGGGCAGGGCCATCAGTTTATccgccg                         >  2:180237/1‑151 (MQ=255)                                                                                                                     cGATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGGGCAGGGCCATCAGTTTATCCGCCgg                        >  2:105120/1‑151 (MQ=255)                                                                                                                      gATCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGGGCAGGGCCATCAGTTTATCCGCCGGa                       <  1:495909/151‑1 (MQ=255)                                                                                                                        tCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGGGCAGGGCCATCAGTTTATCCGCCGGAat                     >  2:374539/1‑151 (MQ=255)                                                                                                                        tCACCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGGGCAGGGCCATCAGTTTATCCGCCGGAat                     >  1:260809/1‑151 (MQ=255)                                                                                                                          aCCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGGGCAGGGCCATCAGTTTATCCGCCGGAatat                   <  2:468595/151‑1 (MQ=255)                                                                                                                          aCCTGATACCCCATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGGGCAGGGCCATCAGTTTATCCGCCGGAatat                   >  1:466613/1‑151 (MQ=255)                                                                                                                                  ccccATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGGGCAGGGCCATCAGTTTATCCGCCGGAATATCCGCTtca           <  2:417759/151‑1 (MQ=255)                                                                                                                                  ccccATATTCAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGGGCAGGGCCATCAGTTTATCCGCCGGAATATCCGCTtca           <  1:145586/151‑1 (MQ=255)                                                                                                                                          ccAGCACCTTCGCTTTCTGCGCCGCCCGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGGGCAGGGCCATCAGTTTATCCGCCGGAATATCCGCTTCATCAGCCt    >  2:597539/2‑150 (MQ=255)                                                                                                                                           cAGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGGGCAGGGCCATCAGTTTATCCGCCGGAATATCCGCTTCATCAGCCt    <  2:566940/149‑1 (MQ=255)                                                                                                                                            aGCACCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGGGCAGGGCCATCAGTTTATCCGCCGGAATATCCGCTTCATCAGCCttt  >  2:208228/1‑150 (MQ=255)                                                                                                                                               |                                                                                                                                                   CGGTGCCGTCGACGATAAACGGTTATGCAACTGCGTAATATCATCATAGTTAAACAAATCAGGAATATAGCTGCGCACAATCTTATTTACATGGGTAGCGATCACGCTGGCGCTGTCGATCACCTGATACCCCATATTCAGCGCCTTCGCTTTCTGCGCCGCCTGGATCCAGGTGACCGGCATCCCGTACGCCGGGTCGTTCCCCTGCACGCCGTCAATCTCGCCGTAGGTTTCGCTGGAGGGCAGGGCCATCAGTTTATCCGCCGGAATATCCGCTTCATCAGCCTTT  >  NC_000913/248892‑249180

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑