Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,231,149	(A)6→5	coding (796/873 nt)	rluF →	23S rRNA pseudouridine(2604) and tRNA(Tyr) pseudouridine(35) synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,231,144	0	A	.	100.0%	207.2 / NA	49	coding (791/873 nt)	rluF	23S rRNA pseudouridine(2604) and tRNA(Tyr) pseudouridine(35) synthase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (25/24);  total (25/24)

CTGGGGGAATGGCGCGATTTAACCGACGATGAGTTAATCGACCTCTTTAAGCTCATTGAAAATTCCTCTTCCGAGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGGAAAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTAACGCCTCAGACTGATGAAAACGGCCCAAAAGTGCCCGGACAGTCCCCTCG  >  NC_000913/4231005‑4231279                                                                                                                                            |                                                                                                                                        cTGGGGGAATGGCGCGATTTAACCGACGATGAGTTAATCGACCTCTTTAAGCTCATTGAAAATTCCTCTTCCGAGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGGa                                                                                                                                         >  1:102120/1‑140 (MQ=255)                            gaTGAGTTAATCGACCTCTTTAAGCTCATTGAAAATTCCTCTTCCGAGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCg                                                                                                             >  2:421672/1‑140 (MQ=255)                                aGTTAATCGACCTCTTTAAGCTCATTGAAAATTCCTCTTCCGAGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAgg                                                                                                                       <  1:826811/126‑1 (MQ=255)                                aGTTAATCGACCTCTTTAAGCTCATTGAAAATTCCTCTTCCGAGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAgg                                                                                                                       >  2:826811/1‑126 (MQ=255)                                    aaTCGACCTCTTTAAGCTCATTGAAAATTCCTCTTCCGAGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTAGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCaa                                                                                                     >  1:434823/1‑140 (MQ=255)                                     aTCGACCTCTTTAAGCTCATTGAAAATTCCTCTTCCGAGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAAc                                                                                                    >  1:228960/1‑140 (MQ=255)                                        gACCTCTTTAAGCTCATTGAAAATTCCTCTTCCGAGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGt                                                                                                 <  2:882216/140‑1 (MQ=255)                                         aCCTCTTTAAGCTCATTGAAAATTCCTCTTCCGAGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTa                                                                                                <  1:610068/140‑1 (MQ=255)                                          ccTCTTTAAGCTCATTGAAAATTCCTCTTCCGAGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTaa                                                                                               >  1:611750/1‑140 (MQ=255)                                          ccTCTTTAAGCTCATTGAAAATTCCTCTTCCGAGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTaa                                                                                               <  1:421672/140‑1 (MQ=255)                                                  aGCTCATTGAAAATTCCTCTTCCGAGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTa                                                                                       <  1:595249/140‑1 (MQ=255)                                                        ttGAAAATTCCTCTTCCGAGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGt                                                                                                 >  1:961706/1‑124 (MQ=255)                                                        ttGAAAATTCCTCTTCCGAGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGt                                                                                                 <  2:961706/124‑1 (MQ=255)                                                        ttGAAAATTCCTCTTCCGAGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGc                                                                                 >  2:341670/1‑140 (MQ=255)                                                        ttGAAAATTCCTCTTCCGAGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGc                                                                                 >  1:1061361/1‑140 (MQ=255)                                                            aaaTTCCTCTTCCGAGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCggg                                                                             <  2:611750/140‑1 (MQ=255)                                                                  ctctTCCGAGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTGACCTCGCCGGGGCGTaa                                                                       >  2:1011797/1‑140 (MQ=255)                                                                       ccGAGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAaaga                                                                  >  2:108276/1‑140 (MQ=255)                                                                          aGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAgg                                                               >  1:307611/1‑140 (MQ=255)                                                                          aGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAgg                                                               >  1:151285/1‑140 (MQ=255)                                                                          aGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAgg                                                               >  2:888443/1‑140 (MQ=255)                                                                          aGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAgg                                                               >  1:840175/1‑140 (MQ=255)                                                                            gTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAgggg                                                             >  2:903511/1‑140 (MQ=255)                                                                            gTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAgggg                                                             <  1:888443/140‑1 (MQ=255)                                                                            gTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTAGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAgggg                                                             <  2:434823/140‑1 (MQ=255)                                                                              aaaaCTTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCCAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGgcg                                                           <  2:1004395/140‑1 (MQ=255)                                                                              aaaaCCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGgcg                                                           <  2:228960/140‑1 (MQ=255)                                                                                aaCCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCt                                                         <  1:1133435/140‑1 (MQ=255)                                                                                   cTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGAt                                                      <  2:151285/140‑1 (MQ=255)                                                                                   cTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGAt                                                      <  2:307611/140‑1 (MQ=255)                                                                                     aaaGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTa                                                    <  1:903511/140‑1 (MQ=255)                                                                                      aaGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTaa                                                   >  2:268350/1‑140 (MQ=255)                                                                                            aGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTAACGCCTc                                             >  1:211752/1‑140 (MQ=255)                                                                                                        aaaCAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTAACGCCTCAGACTGATGaaa                                 >  1:1055584/1‑140 (MQ=255)                                                                                                        aaaCAGCGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTAACGCCTCAGACTGATGaaa                                 >  1:2760/1‑140 (MQ=255)                                                                                                              cGGGCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTAACGCCTCAGACTGATGAAAACGGcc                           >  2:965797/1‑140 (MQ=255)                                                                                                               gggCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTAACGCCTCAGACTGATGAAAACGGccc                          >  1:156994/1‑140 (MQ=255)                                                                                                                ggCATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTAACGCCTCAGACTGATGAAAACGGCCCa                         <  2:156994/140‑1 (MQ=255)                                                                                                                  cATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTAACGCCTCAGACTGATGAAAACGGCCCaaa                       <  1:341670/140‑1 (MQ=255)                                                                                                                  cATCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAACGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTAACGCCTCAGACTGATGAAAACGGCCCaaa                       <  2:1061361/140‑1 (MQ=255)                                                                                                                   aTCAAACGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTAACGCCTCAGACTGATGAAAACGGCCCaaaa                      >  1:84550/1‑140 (MQ=255)                                                                                                                       aaCGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTAACGCCTCAGACTGATGAAAACGGCCCAAAAGTGc                  <  2:84550/140‑1 (MQ=255)                                                                                                                        aCGTCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTAACGCCTCAGACTGATGAAAACGGCCCAAAAGTGcc                 >  2:599617/1‑140 (MQ=255)                                                                                                                           tCCAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTAACGCCTCAGACTGATGAAAACGGCCCAAAAGTGCCCgg              <  2:360526/140‑1 (MQ=255)                                                                                                                            ccAGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTAACGCCTCAGACTGATGAAAACGGCCCAAAAGTGCCCGGa             <  2:1047556/140‑1 (MQ=255)                                                                                                                              aGTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTAACGCCTCAGACTGATGAAAACGGCCCAAAAGTGCCCGGACa           <  2:906440/140‑1 (MQ=255)                                                                                                                               gTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTAACGCCTCAGACTGATGAAAACGGCCCAAAAGTGCCCGGACAg          >  1:39791/1‑140 (MQ=255)                                                                                                                               gTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTAACGCCTCAGACTGATGAAAACGGCCCAAAAGTGCCCGGACAg          <  1:268350/140‑1 (MQ=255)                                                                                                                               gTCGTTAAGATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTAACGCCTCAGACTGATGAAAACGGCCCAAAAGTGCCCGGACAg          >  1:183094/1‑140 (MQ=255)                                                                                                                                       gATGG‑AAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTAACGCCTCAGACTGATGAAAACGGCCCAAAAGTGCCCGGACAGTCCCCTCg  <  2:183094/140‑1 (MQ=255)                                                                                                                                            |                                                                                                                                        CTGGGGGAATGGCGCGATTTAACCGACGATGAGTTAATCGACCTCTTTAAGCTCATTGAAAATTCCTCTTCCGAGGTAAAACCTAAAGCGAAGGCCAAACCGAAAACAGCGGGCATCAAACGTCCAGTCGTTAAGATGGAAAAAACGGCGGAAAAAGGCGGTCGCCCGGCGTCCAACGGTAAGCGTTTTACCTCGCCGGGGCGTAAAAAGAAGGGGCGCTGATTAACGCCTCAGACTGATGAAAACGGCCCAAAAGTGCCCGGACAGTCCCCTCG  >  NC_000913/4231005‑4231279

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑