Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,950,476	(T)8→7	intergenic (+56/‑31)	ilvL → / → ilvX	ilvG operon leader peptide/uncharacterized protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,950,469	0	T	.	100.0%	197.3 / NA	48	intergenic (+49/‑38)	ilvL/ilvX	ilvG operon leader peptide/uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (27/21);  total (27/21)

GAGTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGGCGCACAGTGGGTGGTACATGCGTTGCGGG  >  NC_000913/3950338‑3950596                                                                                                                                    |                                                                                                                                gAGTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGtttttttg                                                                                                                          <  2:368244/139‑2 (MQ=255)   gTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTCTCCCACCGTGCGGGGCTGAACCTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAACACCCCCGCACCGAAAAGGCCGGGGGtttttttgac                                                                                                                        <  2:642730/139‑4 (MQ=255)      aTTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCtt                                                                                                                    >  2:144886/1‑139 (MQ=255)        tAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTaa                                                                                                                  >  2:328972/1‑139 (MQ=255)                    gATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCga                                                                                                      <  1:712848/139‑1 (MQ=255)                     aTTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCgag                                                                                                     >  1:46395/1‑139 (MQ=255)                          cGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCa                                                                                                >  1:228671/1‑139 (MQ=255)                          cGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCa                                                                                                <  1:278995/139‑1 (MQ=255)                          cGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCa                                                                                                <  1:601966/139‑1 (MQ=255)                          cGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑‑TTTTTTGACCTTAAAAACATAACCGAGGAGCAg                                                                                               >  2:526195/1‑139 (MQ=255)                           gtggtggtgATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑‑TTTTTTGACCTTAAAAACATAACCGAGGAGCAGa                                                                                              <  1:526195/139‑1 (MQ=255)                            tggtggtgATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGa                                                                                              <  1:144886/139‑1 (MQ=255)                              gagacagttattaTCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCATGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACa                                                                                            <  2:687237/132‑1 (MQ=255)                                    attattATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAAt                                                                                      >  1:372128/1‑139 (MQ=255)                                              cACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGa                                                                                              <  1:1035254/121‑1 (MQ=255)                                              cACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGa                                                                                              >  2:1035254/1‑121 (MQ=255)                                                ccGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACaaaa                                                                          >  2:537442/1‑139 (MQ=255)                                                ccGTGCGCGGCTGCACTTGGACGAAGAAAGGCTTAGAGATCAAGCCTTAACAAACTAAGACCCCCGCACCGAAAGGACCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGGATAACAGctgtctc                                                                          >  1:687237/1‑133 (MQ=255)                                                  gTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAAtt                                                                        >  2:930980/1‑139 (MQ=255)                                                   tGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTc                                                                       >  1:6527/1‑139 (MQ=255)                                                   tGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTc                                                                       >  1:717573/1‑139 (MQ=255)                                                          cTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTtct                                                                >  1:102025/1‑139 (MQ=255)                                                                 tGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGAtt                                                         <  2:717573/139‑1 (MQ=255)                                                                  ggACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGcaca                                                                             <  2:590680/118‑1 (MQ=255)                                                                  ggACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGcaca                                                                             >  1:590680/1‑118 (MQ=255)                                                                  ggACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑‑TTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCa                                                       >  1:620770/1‑139 (MQ=255)                                                                       aGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGAc                                                   <  1:537442/139‑1 (MQ=255)                                                                              gCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGaac                                            <  2:228671/139‑1 (MQ=255)                                                                                  agagATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACAt                                                                                                            <  1:746058/71‑1 (MQ=255)                                                                                  agagATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACAt                                                                                                            >  2:746058/1‑71 (MQ=255)                                                                                    agaTCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAactaacta                                      >  2:584270/1‑139 (MQ=255)                                                                                        cAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAACACATAACCGAGGAG‑ATACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAAt                                 >  2:805076/1‑139 (MQ=255)                                                                                        cAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGaa                                  >  1:40079/1‑139 (MQ=255)                                                                                         aaGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAAt                                 >  2:1048350/1‑139 (MQ=255)                                                                                              ttAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGgcgc                            <  2:40079/139‑1 (MQ=255)                                                                                               tAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGGCGca                           <  2:6527/139‑1 (MQ=255)                                                                                                aaCGAACTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGGCGcac                          >  1:851083/1‑139 (MQ=255)                                                                                                      cTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGGCGCACAgtggg                    <  1:584270/139‑1 (MQ=255)                                                                                                      cTAAGACCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGGCGCACAgtggg                    <  2:372128/139‑1 (MQ=255)                                                                                                               ccGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTaaaaa                                                                                                               >  2:672826/1‑39 (MQ=37)                                                                                                               ccGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTaaaaa                                                                                                               <  1:672826/39‑1 (MQ=255)                                                                                                               ccGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTaa                                                                                                                  >  2:601478/1‑36 (MQ=37)                                                                                                               ccGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTaa                                                                                                                  <  1:601478/36‑1 (MQ=37)                                                                                                               ccGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGGCGCACAGTGGGTGGTACATg           >  2:370357/1‑139 (MQ=255)                                                                                                               ccGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGGCGCACAGTGGGTGGTACATg           >  1:916373/1‑139 (MQ=255)                                                                                                                     cGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGGTTCAGGACGGGGaa                                             <  1:489338/99‑1 (MQ=255)                                                                                                                     cGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGaa                                             >  2:489338/1‑99 (MQ=255)                                                                                                                      gAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGGCGcaca                         <  1:260638/118‑1 (MQ=255)                                                                                                                      gAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGGCGcaca                         >  2:260638/1‑118 (MQ=255)                                                                                                                        aaGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGGCGCACAGTGGGTGGTACATGCGTTGCggg  <  1:1035760/139‑1 (MQ=255)                                                                                                                                    |                                                                                                                                GAGTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGGCGCACAGTGGGTGGTACATGCGTTGCGGG  >  NC_000913/3950338‑3950596

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑