Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,308,736	C→T	Q63Q (CAG→CAA)	nlpI ←	lipoprotein NlpI

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,308,736	0	C	T	100.0%	107.6 / NA	32	Q63Q (CAG→CAA)	nlpI	lipoprotein NlpI
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (17/15);  total (17/15)

CACGACCGCCGTAATATAATGCGATCCCGCGATTCAAGTGCGCGTAGTTGTAAGTTGGATCAAGCTCAAGTACAGAATCAAACGCTTCATAGGCAGCATCAAAATTGCCTGCCTGCGTTAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGCTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTGCATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGCAAAAAAGGCTTCATTTCCCACTCCCGAAGACCACGGTTGAATGAACGTCCTGTTCCCG  >  NC_000913/3308489‑3308968                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                         cacaaCCGCCGTAATATAATGCGATCCCGCGATTCAAGTGCGCGTAGTTGTAAGTTGGATCAAGCTCAAGTACAGAATCAAACGCTTCATAGGCAGCATCAAAATTGCCTGCCTGCGTTAAATATATTCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAAACTATCATACAACTCTCCGCGCGCATATAAAAGTtgt                                                                                                                                                                                                                                       <  2:228073/247‑1 (MQ=255)                     gCGATCCCGCGATTCAAGTGCGCGTAGTTGTAAGTTGGATCAAGCTCAAGTACAGAATCAAACGCTTCATAGGCAGCATCAAAATTGCCTGCCTGCGTTAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTa                                                                                                                                                                                                                    >  1:259776/1‑250 (MQ=255)                           cagcgATTCAAGTGAGCGTAGTTGGAAGTTGGATTAAGCTCAAGTACAGAATCAACCGCTTCATAGGCAGCATCAAAATTGCCTGCATGCGTTAAATATATGCCTAAGTAATCGAATACTTCAGGCATATCCGGTCGGATTGCCAGAGCTTGCGCAAAATCGTTACGCGCTAATGCCCTAAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAATCCCg                                                                                                                                                                                                             <  2:333866/249‑1 (MQ=255)                                           cgTAGTTGTAAGTTGGATCAAGCTCAAGTACAGAATCAAACGCTTCATAGGCAGCATCAAAATTGCCTGCCTGCGTTAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGt                                                                                                                                                                                             <  2:126266/251‑1 (MQ=255)                                              aGTTGTAAGTTGGATCAAGCTCAAGTACAGAATCAAACGCTTCATAGGCAGCATCAAAATTGCCTGCCTGCGTTAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAACAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTcc                                                                                                                                                                                          >  2:153313/1‑251 (MQ=255)                                                      gTTGGATCAAGCTCAAGTACAGAATCAAACGCTTCATAGGCAGCATCAAAATTGCCTGCCTGCGTTAAATATATGCCTAAGAAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGc                                                                                                                                                                                  >  2:157749/1‑251 (MQ=255)                                                          cgtttgattctgttccAGAATCAAACGCTTCATAGGCAGCATCAAAATTGCCTGCCTGCGTTAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGcc                                                                                                                                                                                 >  1:295857/16‑248 (MQ=255)                                                                gCTCAAGTACAGAATCAAACGCTTCATAGGCAGCATCAAAATTGCCTGCCTGCGTTAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACt                                                                                                                                                                        <  1:80375/251‑1 (MQ=255)                                                                    aaGTACATAATCAAACGCTTCATAGGCAGCATCAAAATTGCCTGCCTGCGTTAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATTCGTGCCAGAATCACTTCct                                                                                                                                                                    <  2:196942/251‑1 (MQ=255)                                                                                           aGGCAGCATCAAAATTGCCTGCCTGCGTTAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGt                                                                                                                                             <  2:176826/251‑1 (MQ=255)                                                                                               agcaTCAAAATTGCCTGCCTGCGTTAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACcg                                                                                                                                         >  2:222486/1‑251 (MQ=255)                                                                                                    cAAAATTGCCTGCCTGCGTTAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCNatg                                                                                                                                    >  2:366375/1‑249 (MQ=255)                                                                                                               gcctgcGTTAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCTGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCAcgc                                                                                                                           <  2:275200/249‑3 (MQ=255)                                                                                                                 ctgcGTTAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGGTGCAATGGTACCGCGAGGACTTCACTTTTAc                                                                                                                       >  2:275661/1‑251 (MQ=255)                                                                                                                   gcGTTAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTAc                                                                                                                       <  1:176995/249‑1 (MQ=255)                                                                                                                    cGTTAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTc                                                                                                                                                         <  2:249390/214‑1 (MQ=255)                                                                                                                    cGTTAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTc                                                                                                                                                         >  1:249390/1‑214 (MQ=255)                                                                                                                       tAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAgg                                                                                                                 >  2:147928/1‑251 (MQ=255)                                                                                                                              atGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCTGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGTTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTAtt                                                                                                          <  1:113137/251‑1 (MQ=255)                                                                                                                                              aTACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTGCATCCTGCAAGc                                                                                          >  1:235693/1‑251 (MQ=255)                                                                                                                                                  ttCAGGCATATCCGGTCGGATTGCCCGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTGCATCCTGCAAGCNTa                                                                                       >  2:353785/1‑250 (MQ=255)                                                                                                                                                               ggTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTGCATCCTGCAAGCGTAAGTGCTGTCGCaa                                                                          >  2:243869/1‑250 (MQ=255)                                                                                                                                                                             cgcTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACGCTCCGCGCTCATATAAAAGTTGTGCGCGGTCGTCATCGGTGAAAGCCCGACTGGCAAGGATTTGTGCCATACGTGCCAGAATCACTTCCTGCGGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTCCGCCAGGAAGTATTACTGCATCCTGCAAGCGTAAGTTCTGTCGTAACGAAACACCAGCGCa                                                           <  2:56951/251‑1 (MQ=255)                                                                                                                                                                                    gAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTGCATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGCAAAAAAgg                                                    >  1:9761/1‑251 (MQ=255)                                                                                                                                                                                    aaaaaaTCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATGCAACACTCCGCGCTTATAGAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGGCTTTGCTTTGACGCCAGGAAGTATTACTGCATCCGGCAAGCGTAAGTGCTGTCGCAGCGGAACACCAGCGCAACAAAgc                                                    <  2:24230/250‑2 (MQ=255)                                                                                                                                                                                          tCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTGCATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGCAAAAAAGGCTTCAt                                              >  1:128730/1‑251 (MQ=255)                                                                                                                                                                                            gTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACCCCCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTGCATCCTGCTAGCGTAAGTGCTGTCGCAACGAAACACCATCGCAAAAAAGGCTTCAttt                                            <  2:195034/251‑1 (MQ=255)                                                                                                                                                                                                cgcgCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTGCATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGCAAAAAAGGCTTCATTTCCCa                                        <  2:9761/251‑1 (MQ=255)                                                                                                                                                                                                   gcTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTGCATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGCAAAAAAGGCTTCATTTCCCACTc                                     >  2:114869/1‑251 (MQ=255)                                                                                                                                                                                                   gcTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTGCATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGCAAAAAAGGCTTCATTTCCCACTc                                     <  1:100899/251‑1 (MQ=255)                                                                                                                                                                                                         gCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTGCATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGCAAAAAAGGCTTCATTTCCCACTCCCGa                                 >  1:40368/1‑249 (MQ=255)                                                                                                                                                                                                                                      tCCGCGCTCATATAAAAGTTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTGCATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGAGCAAAAAAGGCTTCATTTCCCACTCCCGAAGACCACGGATGAATGAACGTCCTGTTCCCg  >  1:261420/1‑251 (MQ=255)                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                         CACGACCGCCGTAATATAATGCGATCCCGCGATTCAAGTGCGCGTAGTTGTAAGTTGGATCAAGCTCAAGTACAGAATCAAACGCTTCATAGGCAGCATCAAAATTGCCTGCCTGCGTTAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGCTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTGCATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGCAAAAAAGGCTTCATTTCCCACTCCCGAAGACCACGGTTGAATGAACGTCCTGTTCCCG  >  NC_000913/3308489‑3308968

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑