Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_bme_pgi	1,194,992	+T	intergenic (‑41/‑131)	rluE ← / → icd	23S rRNA pseudouridine(2457) synthase/isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_bme_pgi	1,194,992	1	.	T	100.0%	223.3 / NA	61	intergenic (‑41/‑131)	rluE/icd	23S rRNA pseudouridine(2457) synthase/isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base T (29/32);  total (29/32)

CAGGTTTACGCCTGGTAGAACGTTGCGAGCTGAATCGCTTAACCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATA‑GGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAACGTGGTGGCAGACGAGCAAACCAGTAGCGCTCGAAGGAGAGGTGAA  >  NC_000913_3_bme_pgi/1194849‑1195123                                                                                                                                                 |                                                                                                                                    cAGGTTTACGCCTGGTAGAACGTTGCGAGCTGAATCGCTTAACCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGgta                                                                                                                                >  2:47350/1‑150 (MQ=255)  aGGTTTACGCCTGGTAGAACGTTGCGAGCTGAATCGCTTAACCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGgtag                                                                                                                               >  3:86968/1‑150 (MQ=255)  aGGTTTACGCCTGGTAGAACGTTGCGAGCTGAATCGCTTAACCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGgtag                                                                                                                               >  1:404034/1‑150 (MQ=255)          gCCTGGTAGAACGTTGCGAGCTGAATCGCTTAACCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACa                                                                                                                       >  2:682223/1‑150 (MQ=255)          gCCTGGTAGAACGTTGCGAGCTGAATCGCTTAACCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACa                                                                                                                       >  2:317320/1‑150 (MQ=255)            cTGGTAGAACGTTGCGAGCTGAATCGCTTAACCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAg                                                                                                                     >  4:186124/1‑150 (MQ=255)             tGGTAGAACGTTGCGAGCTGAATCGCTTAACCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGc                                                                                                                    >  4:345374/1‑150 (MQ=255)                        tGCGAGCTGAATCGCTTAACCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAAt                                                                                                         <  2:480511/150‑1 (MQ=255)                        tGCGAGCTGAATCGCTTAACCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAAt                                                                                                         <  1:62032/150‑1 (MQ=255)                          cGAGCTGAATCGCTTAACCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCa                                                                                                       <  1:47350/150‑1 (MQ=255)                            aGCTGAATCGCTTAACCTGGTGATTTCTAAAAGAAGTTTTTTTTTTTTTTTTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCACACAATATGGGTAGTATTGACAAGCCAATTACAAATCAtt                                                                                                     >  4:368840/1‑150 (MQ=255)                             gCTGAATCGCTTAACCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTa                                                                                                    >  1:686556/1‑150 (MQ=255)                              cTGAATCGCTTAACCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTaa                                                                                                   >  1:28456/1‑150 (MQ=255)                               tGAATCGCTTAACCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAAc                                                                                                  >  1:653393/1‑150 (MQ=255)                                gAATCGCTTAACCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACa                                                                                                 >  1:347207/1‑150 (MQ=255)                                       ttAACCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAAtt                                                                                          <  2:347207/150‑1 (MQ=255)                                       ttAACCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAAAAAAAAAAAAAAAAtt                                                                                          <  4:86968/150‑1 (MQ=255)                                       ttAACCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATACCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAAtt                                                                                          <  2:404034/150‑1 (MQ=255)                                       ttAACCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTACAGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAAAAAATAAAAAAAAAtt                                                                                          <  2:613600/150‑1 (MQ=255)                                         aaCCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGc                                                                                        <  3:275170/150‑1 (MQ=255)                                          aCCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGct                                                                                       <  2:686556/150‑1 (MQ=255)                                             tGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTa                                                                                    <  4:360551/150‑1 (MQ=255)                                                    ttCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATc                                                                             <  3:345374/150‑1 (MQ=255)                                                     tCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATcc                                                                            >  3:32344/1‑150 (MQ=255)                                                       tAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGt                                                                          >  3:424446/1‑150 (MQ=255)                                                       tAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGt                                                                          >  3:424132/1‑150 (MQ=255)                                                             aagTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCa                                                                    >  3:368142/1‑150 (MQ=255)                                                                      gCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCaaa                                                           <  4:424446/150‑1 (MQ=255)                                                                      gCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCaaa                                                           <  4:424132/150‑1 (MQ=255)                                                                       cATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAAc                                                          >  1:509550/1‑150 (MQ=255)                                                                          ggTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCa                                                       <  1:682223/150‑1 (MQ=255)                                                                          ggTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCa                                                       <  2:598169/150‑1 (MQ=255)                                                                                 tCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCaa                                                <  1:317320/150‑1 (MQ=255)                                                                                  cAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAAc                                               >  1:603255/1‑150 (MQ=255)                                                                                         tATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAACGtggtgg                                        <  1:420566/150‑1 (MQ=255)                                                                                         tATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAACGtggtgg                                        <  2:28456/150‑1 (MQ=255)                                                                                           tGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGAc                                                                                                                        <  3:180075/68‑1 (MQ=255)                                                                                           tGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGAc                                                                                                                        >  4:180075/1‑68 (MQ=255)                                                                                           tGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAACGTGGTGGCa                                      >  2:373267/1‑150 (MQ=255)                                                                                              aTTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAACGTGGTGGCAGAc                                   <  3:383708/150‑1 (MQ=255)                                                                                                tGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAACGTGGTGGCAGACGa                                 <  4:368142/150‑1 (MQ=255)                                                                                                  ccGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAACGTGGTGGCAGACgcgc                               >  4:326205/1‑150 (MQ=255)                                                                                                  ccGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAACGTGGTGGCAGACGAGc                               <  2:603255/150‑1 (MQ=255)                                                                                                   cGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAACGTGGTGGCAGACGAGCa                              >  4:411853/1‑150 (MQ=255)                                                                                                   cGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAACGTGGTGGCAGACGAGCa                              >  1:378918/1‑150 (MQ=255)                                                                                                    gCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAACGTGGTGGCAGACGAGCaa                             >  4:158822/1‑150 (MQ=255)                                                                                                     cATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCTTATGCAACGTGGTGGCAGACGAGCaaa                            <  1:509758/150‑1 (MQ=255)                                                                                                     cATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCGTATGCAACGTGGTGGCAGACGAGCaaa                            <  1:509632/150‑1 (MQ=255)                                                                                                        tataGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCg                                                                      <  3:75877/105‑1 (MQ=255)                                                                                                        tataGCCTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCg                                                                      >  4:75877/1‑105 (MQ=255)                                                                                                             ccTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAACGTGGTGGCAGACGAGCAAACCAGTAgc                    >  2:314525/1‑150 (MQ=255)                                                                                                             ccTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAACGTGGTGGCAGACGAGCAAACCAGTAgc                    <  2:203197/150‑1 (MQ=255)                                                                                                              cTAATAACGCGCATCTTTCATGACGGCAAACAATATGGGTAGTACTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAACGTGGTGGCAGACGAGCAAACCAGTAgcg                   >  2:485327/1‑150 (MQ=255)                                                                                                                    aCGCGCATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAACGTGGTGGCAGACGAGCAAACCAGTAGCGCTCGaa             <  2:516702/150‑1 (MQ=255)                                                                                                                       cgcATCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAACGTGGTGGCAGACGAGCAAACCAGTAGCGCTCGAAGga          <  1:373267/150‑1 (MQ=255)                                                                                                                          aTCTTTCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAACGTGGTGGCAGACGAGCAAACCAGTAGCGCTCGAAGGagag       <  3:186124/150‑1 (MQ=255)                                                                                                                               tCATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAACGTGGTGGCAGACGAGCAAACCAGTAGCGCTCGAAGGAGAGGTGaa  <  2:378918/150‑1 (MQ=255)                                                                                                                                cATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAAc                                               <  4:313321/104‑1 (MQ=255)                                                                                                                                cATGACGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAAc                                               >  3:313321/1‑104 (MQ=255)                                                                                                                                    aCGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACaaaaaa                                                                                            <  4:351610/55‑1 (MQ=255)                                                                                                                                    aCGGCAAACAATATGGGTAGTATTGACAAGCCAATTACAAATCATTAACaaaaaa                                                                                            >  3:351610/1‑55 (MQ=255)                                                                                                                                                 |                                                                                                                                    CAGGTTTACGCCTGGTAGAACGTTGCGAGCTGAATCGCTTAACCTGGTGATTTCTAAAAGAAGTTTTTTGCATGGTATTTTCAGAGATTATGAATTGCCGCATTATAGCCTAATAACGCGCATCTTTCATGACGGCAAACAATA‑GGGTAGTATTGACAAGCCAATTACAAATCATTAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGGACGCAAACGCATATGCAACGTGGTGGCAGACGAGCAAACCAGTAGCGCTCGAAGGAGAGGTGAA  >  NC_000913_3_bme_pgi/1194849‑1195123

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑