Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,960,118:1	+C	28.3%	coding (1676/2247 nt)	ptsP ←	fused PTS enzyme: PEP‑protein phosphotransferase (enzyme I)/GAF domain containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,960,118	1	.	C	28.3%	72.2 / 72.9	46	coding (1676/2247 nt)	ptsP	fused PTS enzyme: PEP‑protein phosphotransferase (enzyme I)/GAF domain containing protein
Reads supporting (aligned to +/- strand):  ref base . (20/13);  new base C (6/7);  total (26/20)
Fisher's exact test for biased strand distribution p-value = 5.11e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.85e-01

TGCGGCAGCATAAATACCATTGACGGCACTTCCAGCATGATGCCGATACGTGGTTTGGGAATTTCGTAACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATCGGCAT  >  CP009273/2959974‑2960263                                                                                                                                                  |                                                                                                                                                  tGCGGCAGCATAAATACCATTGACGGCACTTCCAGCATGATGCCGATACGTGGTTTGGGAATTTCGTAACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑cccat                                                                                                                                              >  1:684372/1‑147 (MQ=255)        gcaTAAATACCATTGACGGCACTTCCAGCATGATGCCGATACGTGGTTTGGGAATTTCGTAACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCaa                                                                                                                                         >  1:325569/1‑148 (MQ=255)        gcaTAAATACCATTGACGGCACTTCCAGCATGATGCCGATACGTGGTTTGGGAATTTCGTAACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCaa                                                                                                                                         >  2:886421/1‑148 (MQ=255)                aCCATTGACGGCACTTCCAGCATGATGCCGATACGTGGTTTGGGAATTTCGTAACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGACCCATCGGCAACAGAATAtt                                                                                                                                >  2:580957/1‑150 (MQ=255)                 ccATTGACGGCACTTCCAGCATGATGCCGATACGTGGTTTGGGAATTTCGTAACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTc                                                                                                                               <  2:289360/149‑1 (MQ=255)                  cATTGACGGCACTTCCAGCATGATGCCGATACGTGGTTTGGGAATTTCGTAACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAg                                                                                                                             >  2:932186/1‑150 (MQ=255)                    ttGACGGCACTTCCAGCATGATGCCGATACGTGGTTTGGGAATTTCGTAACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGACCCATCGGCAACAGAATATTCAgg                                                                                                                            <  1:584213/150‑1 (MQ=255)                       aCGGCACTTCCAGCATGATGCCGATACGTGGTTTGGGAATTTCGTAACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGc                                                                                                                        <  2:220383/150‑1 (MQ=255)                        cGGCACTTCCAGCATGATGCCGATACGTGGTTTGGGAATTTCGTAACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGcc                                                                                                                       >  1:754879/1‑150 (MQ=255)                         ggCACTTCCAGCATGATGCCGATACGTGGTTTGGGAATTTCGTAACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGccc                                                                                                                      <  1:376347/150‑1 (MQ=255)                          gCACTTCCAGCATGATGCCGATACGTGGTTTGGGAATTTCGTAACCGCTCATCTCCTCGCCTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCATCTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCg                                                                                                                     <  1:705429/150‑1 (MQ=255)                            aCTTCCAGCATGATGCCGATACGTGGTTTGGGAATTTCGTAACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTa                                                                                                                   <  2:898123/150‑1 (MQ=255)                                  aGCATGATGCCGATACGTGGTTTGGGAATTTCGTAACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCa                                                                                                             <  2:830909/150‑1 (MQ=255)                                  aGCATGATGCCGATACGTGGTTTGGGAATTTCGTAACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCa                                                                                                             <  2:902312/150‑1 (MQ=255)                                           ccGATACGTGGTTTGGGAATTTCGTAACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACg                                                                                                     >  2:670862/1‑149 (MQ=255)                                                 cGTGGTTTGGGAATTTCGTAACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGACCCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCAt                                                                                               <  2:397697/150‑1 (MQ=255)                                                    ggTTTGGGAATTTCGTAACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGcc                                                                                           >  1:267091/1‑150 (MQ=255)                                                      tttGGGAATTTCGTAACCGATCATCCCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCg                                                                                         >  1:364830/1‑150 (MQ=255)                                                          ggAATTTCGTAACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCAcc                                                                                     >  1:908739/1‑150 (MQ=255)                                                                  gTAACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCTGCACCTGGATCa                                                                              <  1:481415/149‑1 (MQ=255)                                                                     aCCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGACCCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCaaga                                                                           <  1:580957/150‑1 (MQ=255)                                                                        gATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCaag                                                                            >  1:202995/1‑145 (MQ=255)                                                                        gATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGAt                                                                       <  1:875301/150‑1 (MQ=255)                                                                           catcTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGACCCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGAtct                                                                     >  1:634352/1‑150 (MQ=255)                                                                           catcTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGAtctc                                                                    >  2:453061/1‑150 (MQ=255)                                                                            atcTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGACCCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGAtctc                                                                    >  1:600189/1‑150 (MQ=255)                                                                              ctcctcGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCgg                                                                 >  2:288139/1‑150 (MQ=255)                                                                                cctcGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCt                                                               >  1:408529/1‑150 (MQ=255)                                                                                          aCGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGACCCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCg                                                      >  1:184134/1‑150 (MQ=255)                                                                                              ccGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGACCCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAAt                                                  >  2:208312/1‑150 (MQ=255)                                                                                                 gCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCg                                               >  2:184701/1‑149 (MQ=255)                                                                                                        cAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGACCCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATccc                                         <  2:684372/149‑1 (MQ=255)                                                                                                          aTCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGc                                     >  1:921113/1‑150 (MQ=255)                                                                                                            cAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGACCCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGc                                     >  1:196088/1‑149 (MQ=255)                                                                                                               gcggcgTGCTTCATCAACTTCATCGAGGCTTGTGACCCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAAc                                 <  2:113284/150‑1 (MQ=255)                                                                                                                 ggcgTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAAcc                                >  1:857921/1‑148 (MQ=255)                                                                                                                  gcgTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAg                             <  2:857921/150‑1 (MQ=255)                                                                                                                       cTTCATCAACTTCATCGAGGCTTGTGACCCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCAt                         <  2:634352/150‑1 (MQ=255)                                                                                                                        ttCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATg                        >  2:469045/1‑149 (MQ=255)                                                                                                                                   cATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTc              <  1:308099/148‑1 (MQ=255)                                                                                                                                       gAGGCTTGTGACCCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTg          <  2:196088/149‑1 (MQ=255)                                                                                                                                        aGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATc       <  1:453061/150‑1 (MQ=255)                                                                                                                                        aGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATc       >  1:820483/1‑150 (MQ=255)                                                                                                                                          gCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATCgg     >  2:131872/1‑150 (MQ=255)                                                                                                                                          gCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATCgg     >  1:358908/1‑150 (MQ=255)                                                                                                                                             tgtgA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATCGGCAt  >  2:18674/1‑150 (MQ=255)                                                                                                                                              gtgA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATCGGCAt  <  1:886421/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                  TGCGGCAGCATAAATACCATTGACGGCACTTCCAGCATGATGCCGATACGTGGTTTGGGAATTTCGTAACCGATCATCTCCTCGACTTCACGTCCGGCACGTTCAATCAGGCGGCGTGCTTCATCAACTTCATCGAGGCTTGTGA‑CCATCGGCAACAGAATATTCAGGTTGCCCGTAGCGGCATTAGCACGCAGCATCGCCCGCACCTGGATCAAGAAGATCTCCGGCTGATCGAGCGTAATGCGAATCCCACGCCAACCCAGGCATGGATTCTCTTCGCTGATCGGCAT  >  CP009273/2959974‑2960263

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑