Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	270,495	(A)5→4	pseudogene (218/263 nt)	insN →	CP4‑6 prophage; IS911A regulator fragment

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	270,491	0	A	.	100.0%	175.4 / NA	41	pseudogene (214/263 nt)	insN	CP4‑6 prophage; IS911A regulator fragment
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (21/20);  total (21/20)

GGCAGATGCAGCCAGCGCTATGGATGTCGGCCTTTCCACAATGACGCGATGGGTGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGGAAAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAATGAGACGAACAT  >  NC_000913/270352‑270615                                                                                                                                            |                                                                                                                             ggCAGATGCAGCCAGCGCTATGGATGTCGGCCTTTCCACAATGACGCGATGGGTGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGGa                                                                                                                              <  2:259025/140‑1 (MQ=255)  gCAGATGCAGCCAGCGCTATGGATGTCGGCCTTTCCACAATGACGCGATGGGTGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGGaa                                                                                                                             <  1:604385/140‑1 (MQ=255)          agccagcGCTATGGATGTCGGCCTTTCCACAATGACGCGATGGGTGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACa                                                                                                                    <  2:384345/140‑1 (MQ=255)          agccagcGCTATGGATGTCGGCCTTTCCACAATGACGCGATGGGTGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACa                                                                                                                    <  2:140723/140‑1 (MQ=255)                cgcTATGGATGTCGGCCTTTCCACAATGACGCGATGGGTGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTAt                                                                                                              >  1:334604/1‑140 (MQ=255)                    aTGGATGTCGGCCTTTCCACAATGACGCGATGGGTGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGaa                                                                                                          <  2:672117/140‑1 (MQ=255)                         tGTCGGCCTTTCCACAATGACGCGATGGGTGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGa                                                                                                     <  2:334604/140‑1 (MQ=255)                          gTCGGCCTTTCCACAATGACGCGATGGGTGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGaa                                                                                                    >  2:450797/1‑140 (MQ=255)                          gTCGGCCTTTCCACAATGACGCGATGGGTGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGaa                                                                                                    >  1:692487/1‑140 (MQ=255)                          gTCGGCCTTTCCACAATGACGCGATGGGTGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGaa                                                                                                    >  1:814090/1‑140 (MQ=255)                               ccTTTCCACAATGACGCGATGGGTGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGa                                                                                               >  2:542235/1‑140 (MQ=255)                                  ttCCACAATGACGCGATGGGTGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAat                                                                                            >  2:455123/1‑140 (MQ=255)                                  ttCCACAATGACGCGATGGGTGAAACAATTACGTGATGAACGGCAAGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTAAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAat                                                                                            >  2:758827/1‑140 (MQ=255)                                        aaTGACGCGATGGGTGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTaaa                                                                                      <  1:545689/140‑1 (MQ=255)                                         aTGACGCGATGGGTGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTaaaa                                                                                     >  1:1081933/1‑140 (MQ=255)                                             cgcgATGGGTGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAgg                                                                                 >  1:365906/1‑140 (MQ=255)                                             cgcgATGGGTGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAgg                                                                                 >  1:638227/1‑140 (MQ=255)                                              gcgATGGGTGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGc                                                                                <  1:455123/140‑1 (MQ=255)                                                    ggTGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGt                                                                          >  1:451871/1‑140 (MQ=255)                                                      tGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAg                                                                        >  1:351399/1‑140 (MQ=255)                                                           cAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCa                                                                   <  1:373536/140‑1 (MQ=255)                                                              ttACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAAtt                                                                >  2:342139/1‑140 (MQ=255)                                                              ttACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAAtt                                                                >  1:496798/1‑140 (MQ=255)                                                                 cGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGt                                                             <  2:351399/140‑1 (MQ=255)                                                                    gatgaACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCaa                                                          >  2:846688/1‑140 (MQ=255)                                                                       gaACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCAACGc                                                       <  2:496798/140‑1 (MQ=255)                                                                         aCGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCAACGCaa                                                     <  1:772473/140‑1 (MQ=255)                                                                                ggCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCAACGCAACAGTTAt                                              >  2:162285/1‑140 (MQ=255)                                                                                 gCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCAACGCAACAGTTAtg                                             <  2:252973/140‑1 (MQ=255)                                                                                  cAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCAACGCAACAGTTAtgt                                            <  2:692487/140‑1 (MQ=255)                                                                                   aaaaCACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCAACGCAACAGTTAtgtg                                           <  1:542235/140‑1 (MQ=255)                                                                                                    ccccATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCgg                          >  2:220626/1‑140 (MQ=255)                                                                                                    ccccATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCgg                          >  1:689865/1‑140 (MQ=255)                                                                                                     cccATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGa                         <  1:846688/140‑1 (MQ=255)                                                                                                         ttACCCCGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGtt                     >  1:764910/1‑140 (MQ=255)                                                                                                              ccGGAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTg                <  1:450797/140‑1 (MQ=255)                                                                                                                ggAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGaa              <  2:638227/140‑1 (MQ=255)                                                                                                                ggAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGaa              <  2:365906/140‑1 (MQ=255)                                                                                                                ggAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGaa              <  1:342139/140‑1 (MQ=255)                                                                                                                 gAACAAATTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAAt             >  1:971492/1‑140 (MQ=255)                                                                                                                     aaaTTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAATgaga         <  2:814090/140‑1 (MQ=255)                                                                                                                       aTTGAAATCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAATGAGACg       <  2:971492/140‑1 (MQ=255)                                                                                                                            aaTCCGTGAGCTCAGG‑AAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAATGAGACGAACAt  >  2:744063/1‑140 (MQ=255)                                                                                                                                            |                                                                                                                             GGCAGATGCAGCCAGCGCTATGGATGTCGGCCTTTCCACAATGACGCGATGGGTGAAACAATTACGTGATGAACGGCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGGAAAAAGCTACAACGTATTGAAATGGAAAATGAAATATTAAAAAAGGCTACTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAATGAGACGAACAT  >  NC_000913/270352‑270615

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑