Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,738,440	T→A	9.2%	V251V (GTA→GTT)	PP_1532 ←	putative Phage integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,738,440	0	T	A	9.2%	157.3 / 5.7	54	V251V (GTA→GTT)	PP_1532	putative Phage integrase
Reads supporting (aligned to +/- strand):  ref base T (22/27);  new base A (3/2);  total (25/29)
Fisher's exact test for biased strand distribution p-value = 6.53e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAATGAAGCAATGTCCTCGCGGCGCTGCCCGGTTATAAGAGCGAGCTCCATGGCGCGCTTGAGC  >  NC_002947/1738296‑1738584                                                                                                                                                 |                                                                                                                                                 tttGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGc                                                                                                                                              >  2:309022/1‑149 (MQ=255)     cTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGt                                                                                                                                          >  6:229157/1‑149 (MQ=255)       gATTGTGTCGAGCATGATGGGAGATACCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGAACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTga                                                                                                                                        >  7:67512/1‑148 (MQ=255)        aTTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTg                                                                                                                                         <  1:309022/147‑1 (MQ=255)        aTTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGc                                                                                                                                        <  8:231662/148‑1 (MQ=255)        aTTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGc                                                                                                                                        <  6:262047/148‑1 (MQ=255)        aTTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTAACGCTggaat                                                                                                                                        <  5:243448/148‑4 (MQ=255)           gtgtCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGa                                                                                                                                     <  6:203704/148‑1 (MQ=255)               cGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCt                                                                                                                                 >  2:114568/1‑148 (MQ=255)                gAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTAACGCTggaa                                                                                                                                         >  6:165086/1‑137 (MQ=255)                gAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTAACGCTggaa                                                                                                                                         <  5:165086/139‑3 (MQ=255)                     tgatgGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCt                                                                                                                                       <  4:184523/136‑1 (MQ=255)                     tgatgGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCt                                                                                                                                       >  3:184523/1‑136 (MQ=255)                       atgGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGc                                                                                                                        <  5:229157/149‑1 (MQ=255)                       atgGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGGGGTGGACCAGGTGCTTTGACAGCACCCGATCGCGGCTACGCCGTATCACTTCACCCAAGATCAGGCTGATGCATTCCACCTTTACGCTGGTGCTGAGCCTTAGCCTGGc                                                                                                                        <  6:86338/149‑1 (MQ=255)                           gagaTCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGccccc                                                                                                                    >  8:143895/1‑149 (MQ=255)                               tCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCt                                                                                                                <  6:51479/149‑1 (MQ=255)                                    ccTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGAt                                                                                                           <  5:40187/149‑1 (MQ=255)                                    ccTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGAt                                                                                                           <  1:114568/149‑1 (MQ=255)                                     cTTCGCGCAGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGAtt                                                                                                          <  8:25179/149‑1 (MQ=255)                                            cgGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGgacgac                                                                                                   <  1:87181/149‑1 (MQ=255)                                                  aTTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAg                                                                                             <  7:143895/149‑1 (MQ=255)                                                         ggtggtggtGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCg                                                                                      >  4:293271/1‑149 (MQ=255)                                                                gtgCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCt                                                                               <  7:134944/149‑1 (MQ=255)                                                                   gatcgggTGCTGTCAAAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCAt                                                                            >  7:6085/6‑149 (MQ=255)                                                                         gTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTa                                                                                                                               >  7:510/1‑92 (MQ=255)                                                                         gTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTa                                                                                                                               <  8:510/92‑1 (MQ=255)                                                                         gTGCTGTCAAAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTACGATTGGACGCCCTGCAGGAATCCGTCCACCTCATCCCgg                                                                       >  4:131522/1‑148 (MQ=255)                                                                          tGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGaa                                                                     <  7:39577/149‑1 (MQ=255)                                                                          tGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGa                                                                      >  3:268527/1‑148 (MQ=255)                                                                                 aCAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAAt                                                              >  6:53327/1‑149 (MQ=255)                                                                                    gCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAATGaa                                                           <  3:293271/149‑1 (MQ=255)                                                                                       cccGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGGCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAATGAAGc                                                         >  4:200228/1‑148 (MQ=255)                                                                                         cGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCACTCCAGCGTTACGCTGGTGCTGATCCTTACCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAATGAAGCAAt                                                      >  1:229037/1‑149 (MQ=255)                                                                                                 gCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAATGAAGCAATGTCCTcgc                                              >  5:129491/1‑149 (MQ=255)                                                                                                 gCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAATGAAGCAATGTCCTcgc                                              <  3:200228/149‑1 (MQ=255)                                                                                                   aaCGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCACCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAAAGAATGAAGCAATGTCCTCgcgg                                            >  5:246226/1‑149 (MQ=255)                                                                                                         gTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAATGAAGCAATGTCCTCGCGGCGCTGc                                      <  4:268527/149‑1 (MQ=255)                                                                                                              aCTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAATGAAGCAATGTCCTCGCGGCGCTGCCCGGt                                 >  3:189225/1‑149 (MQ=255)                                                                                                               cTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAATGAAGCAATGTCCTCGCGGCGCTGCCCGGtt                                <  7:35266/149‑1 (MQ=255)                                                                                                               cTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCCATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAAAGAAGCAATGTACACCCGGCGCAGCACGGt                                 >  7:277547/1‑148 (MQ=255)                                                                                                                ttCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGa                                                                      >  5:151802/1‑110 (MQ=255)                                                                                                                ttCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGa                                                                      <  6:151802/110‑1 (MQ=255)                                                                                                                ttCACACAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAATGAAGCAATGTCCTCGCGGCGCTGCCCGGTta                               >  7:292564/1‑149 (MQ=255)                                                                                                                  cACCCAATCTCAGGCTGATGCATTCCAGCGTTACGCTGTTGCTGATCCTTAGCATGGCCCCCGTCTTCTATTGTACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAATGAAGCAATGTCCTCGCGGCGCTGCCCGGTtat                              <  8:67512/148‑1 (MQ=255)                                                                                                                  cACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAATGAAGCAATGTCCTCGCGGCGCTGCCCGGTtat                              <  4:189225/148‑1 (MQ=255)                                                                                                                   aCCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCAc                                                                                 <  7:186958/96‑1 (MQ=255)                                                                                                                   aCCCAAGCTAAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCAc                                                                                 >  8:186958/1‑96 (MQ=255)                                                                                                                        aGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAATGAAGCAATGTCCTCGCGGCGCTGCCCGGTTATAAgagcg                       <  6:129491/149‑1 (MQ=255)                                                                                                                           tCAGGCTGCTGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAATGAAGCAATg                                                     <  2:213193/116‑1 (MQ=255)                                                                                                                                        caccAGCGTAACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAATGAAGCAATGTCCTCGCGGCGCTGCCCGGTTATAAGAGCGAGCTCCATGGCGCGCt       >  6:132376/3‑149 (MQ=255)                                                                                                                                        caccAGCGTAACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAATGAAGCAATGTCCTCGCGGCGCTGCCCGGTTATAAGAGCGAGCTCCATGGCGCGCt       >  4:62519/3‑149 (MQ=255)                                                                                                                                           cAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAATGAAGCAATGTCCTCGCGGCGCTGCCCGGTTATAAGAGCGAGCTCCATGGCGCGCtt      >  7:293135/1‑147 (MQ=255)                                                                                                                                             gCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAATGAAGCAATGTCCTCGCGGCGCTGCCCGGTTATAAGAGCGAGCTCCATGGCGCGCTTGAGc  <  8:292564/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                 TTTGCTGATTGTGTCGAGCATGATGGGAGATCCCGCCTTCGCGCGGCTGATTGTCCGGTGGTGGTGCACCAGGTGCTTTGACAGCACCCGATCGCGGCAACGCCGTATCACTTCACCCAAGCTCAGGCTGATGCATTCCAGCGTTACGCTGGTGCTGATCCTTAGCCTGGCCCCCGTCTTCGATTGGACGACCTGCAGGAATCCGTCCACCTCATCCCGGAAAACGAATGAAGCAATGTCCTCGCGGCGCTGCCCGGTTATAAGAGCGAGCTCCATGGCGCGCTTGAGC  >  NC_002947/1738296‑1738584

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑