Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,179,038	A→C	K54Q (AAA→CAA)	rplA →	50S ribosomal subunit protein L1

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,179,038	0	A	C	100.0%	188.6 / NA	51	K54Q (AAA→CAA)	rplA	50S ribosomal subunit protein L1
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (32/19);  total (32/19)

CAAGCGCATGCGTGTTATCCGCGAGAAAGTTGATGCAACCAAACAGTACGACATCAACGAAGCTATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTAAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAGCTGCTAAAGCTGCAGGCGCAGAACTGGTAGGTATGGAAGATCTGGC  >  NC_000913/4178893‑4179180                                                                                                                                                  |                                                                                                                                               cAAGCGCATGCGTGTTATCCGCGAGAAAGTTGATGCAACCAAACAGTACGACATCAACGAAGCTATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCt                                                                                                                                           >  1:347485/1‑151 (MQ=255)   aGCGCATGCGTGTTATCCGCGAGAAAGTTGATGCAACCAAACAGTACGACATCAACGAAGCTATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTg                                                                                                                                          >  1:755969/1‑150 (MQ=255)    gcgcATGCGTGTTATCCGCGAGAAAGTTGATGCAACCAAACAGTACGACATCAACGAAGCTATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGAc                                                                                                                                        >  1:71776/1‑151 (MQ=255)      gcATGCGTGTTATCCGCGAGAAAGTTGATGCAACCAAACAGTACGACATCAACGAAGCTATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGAcc                                                                                                                                       >  1:573126/1‑150 (MQ=255)        aTGCGTGTTATCCGCGAGAAAGTTGATGCAACCAAACAGTACGACATCAACGAAGCTATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGa                                                                                                                                    <  1:28308/151‑1 (MQ=255)           cGTGTTATCCGCGAGAAAGTTGATGCAACCAAACAGTACGACATCAACGAAGCTATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAacg                                                                                                                                 >  2:91555/1‑151 (MQ=255)                        agaAAGTTGATGCAACCAAACAGTACGACATCAACGAAGCTATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAAc                                                                                                                    >  1:385793/1‑151 (MQ=255)                         gaAAGTTGATGCAACCAAACAGTACGACATCAACGAAGCTATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGGCCAGAACGTACGTGGTGCAAc                                                                                                                    <  1:768641/150‑1 (MQ=255)                          aaaGTTGATGCAACCAAACAGTACGACATCAACGAAGCTATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTg                                                                                                                  <  1:504488/151‑1 (MQ=255)                                   gCAACCAAACAGTACGACATCAACGAAGCTATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGc                                                                                                         <  1:348713/151‑1 (MQ=255)                                     aaCCAAACAGTACGACATCAACGAAGCTATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCAc                                                                                                       >  2:745038/1‑151 (MQ=255)                                       ccAAACAGTGCGACATCAACGAAGCTATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACgg                                                                                                     <  2:139003/151‑1 (MQ=255)                                          aaCAGTACGACATCAACGAAGCTATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTAc                                                                                                  <  2:410385/151‑1 (MQ=255)                                               tACGACATCAACGAAGCTATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGcc                                                                                             >  1:472103/1‑151 (MQ=255)                                                     aTCAACGAAGCTATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGccgttccg                                                                                       >  2:685254/1‑151 (MQ=255)                                                     aTCAACGAAGCTATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGccgttccg                                                                                       >  2:370573/1‑151 (MQ=255)                                                         acaaaGCTATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTcg                                                                                   >  2:178259/4‑151 (MQ=255)                                                           gAAGCTATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTcgcg                                                                                 >  1:703060/1‑151 (MQ=255)                                                                tATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGcc                                                                            >  1:318782/1‑151 (MQ=255)                                                                      aCTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTAttt                                                                      >  1:73596/1‑151 (MQ=255)                                                                      aCTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTAttt                                                                      >  1:336272/1‑151 (MQ=255)                                                                         gctgAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTa                                                                     <  2:479799/149‑1 (MQ=255)                                                                            gAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCaa                                                                <  1:58117/151‑1 (MQ=255)                                                                               agagCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAgg                                                              >  1:372713/1‑150 (MQ=255)                                                                               agagCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCCGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGt                                                             <  2:47144/151‑1 (MQ=255)                                                                                  gCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCATCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGc                                                           >  2:456722/1‑150 (MQ=255)                                                                                     ggCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCaa                                                         <  2:654125/149‑1 (MQ=255)                                                                                     ggCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAAc                                                       >  2:706593/1‑151 (MQ=255)                                                                                        gACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCt                                                    >  1:831054/1‑151 (MQ=255)                                                                                            gCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGaa                                                 <  2:808418/150‑1 (MQ=255)                                                                                            gCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGa                                                  >  2:534702/1‑149 (MQ=255)                                                                                            gCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAg                                                <  1:499416/151‑1 (MQ=255)                                                                                                aaTTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAgctgc                                            <  1:548400/151‑1 (MQ=255)                                                                                                 aTTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAgctgct                                           <  1:609533/151‑1 (MQ=255)                                                                                                   tCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAGCTGCTa                                          >  2:467081/1‑150 (MQ=255)                                                                                                     gTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAGCTGCTAAAg                                       <  1:219911/151‑1 (MQ=255)                                                                                                      tAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAGCTGCTAAAGc                                      >  1:194367/1‑151 (MQ=255)                                                                                                        gAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAGCTGCTAAAGCTg                                    >  2:329857/1‑151 (MQ=255)                                                                                                             cGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAGCTGCTAAAGCTGCAGgc                               >  2:615294/1‑151 (MQ=255)                                                                                                                 gACGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAGCTGCTAAAGCTGCAGgcgc                             >  2:519004/1‑149 (MQ=255)                                                                                                                  aCGTAGCTGTTAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAGCTGCTAAAGCTGCAGgcgc                             >  2:415577/1‑148 (MQ=255)                                                                                                                           ttAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAGCTGCTAAAGCTGCAGGCGCAGAACTggtagg                 >  1:755215/1‑151 (MQ=255)                                                                                                                            tAACCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAGCTGCTAAAGCTGCAGGCGCAGAACTggtagg                 >  2:581758/1‑150 (MQ=255)                                                                                                                             aaCCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAGCTGCTAAAGCTGCAGGCGCAGAACTggtaggta               <  2:472602/151‑1 (MQ=255)                                                                                                                              aCCTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAGCTGCTAAAGCTGCAGGCGCAGAACTGGTAGGTAt              <  1:890258/151‑1 (MQ=255)                                                                                                                                cTCGGCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAGCTGCTAAAGCTGCAGGCGCAGAACTGGTAGGTATgg            >  1:279084/1‑151 (MQ=255)                                                                                                                                   ggCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAGCTGCTAAAGCTGCAGGCGCAGAACTGGTAGGTATGGa           >  2:427889/1‑149 (MQ=255)                                                                                                                                   ggCATCGACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAGCTGCTAAAGCTGCAGGCGCAGAACTGGTAGGTATGGa           >  1:668910/1‑149 (MQ=255)                                                                                                                                         gACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAGCTGCTAAAGCTGCAGGCGCAGAACTGGTAGGTATGGAAGAGCTgg   >  1:267263/1‑151 (MQ=255)                                                                                                                                         gACGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAGCTGCTAAAGCTGCAGGCGCAGAACTGGTAGGTATGGAAGAGCTgg   <  2:84240/151‑1 (MQ=255)                                                                                                                                          aCGCTCGTCAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAGCTGCTAAAGCTGCAGGCGCAGAACTGGTAGGTATGGAAGAGCTGGc  <  1:274974/151‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                               CAAGCGCATGCGTGTTATCCGCGAGAAAGTTGATGCAACCAAACAGTACGACATCAACGAAGCTATCGCACTGCTGAAAGAGCTGGCGACTGCTAAATTCGTAGAAAGCGTGGACGTAGCTGTTAACCTCGGCATCGACGCTCGTAAATCTGACCAGAACGTACGTGGTGCAACTGTACTGCCGCACGGTACTGGCCGTTCCGTTCGCGTAGCCGTATTTACCCAAGGTGCAAACGCTGAAGCTGCTAAAGCTGCAGGCGCAGAACTGGTAGGTATGGAAGATCTGGC  >  NC_000913/4178893‑4179180

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑