Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	6,040,794	T→A	11.1%	intergenic (+19/+15)	PP_5292 → / ← PP_5293	catabolite repression control protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	6,040,794	0	T	A	11.1%	144.4 / 7.8	54	intergenic (+19/+15)	PP_5292/PP_5293	catabolite repression control protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (24/24);  new base A (3/3);  total (27/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.59e-01

GGTTCGACTACCAGATCCTCACCCCGGGCCTGCGCCGCTTCGTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCGATG‑ATGATCAATATCATCACTGCCACCGTGAGCATGGCAAACAGCACCAGCCCGATAAACACGAA  >  NC_002947/6040648‑6040940                                                                                                                                                   |                                                                                                                                                    ggTTCGACTACCAGATCCTCACCCCGGGCCTGCGCCGCTTCGTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTg                                                                                                                                                   >  3:161089/1‑149 (MQ=255)   ttCGACTACCAGATCCTCACCCCGGGCCTGCGCCGCTTCGTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCa                                                                                                                                                 <  4:161089/149‑1 (MQ=255)           ccAGATCCTCACCCCGGGCCTGCGCCGCTTCGTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAAt                                                                                                                                         >  4:235265/1‑149 (MQ=255)           ccAGATCCTCACCCCGGGCCTGCGACGCTTCGTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGATGACCAACTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAAt                                                                                                                                         >  7:165570/1‑149 (MQ=255)            cAGATCCTCACCCCGGGCCTGCGCCGCTTCGTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACAGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATg                                                                                                                                        >  8:12682/1‑149 (MQ=255)             aGATCCTCACCCCGGGCCTGCGCCGCTTCGTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATgg                                                                                                                                       >  7:114847/1‑149 (MQ=255)                   tCACCCCGGGCCTGCGCCGCTTCGTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAAt                                                                                                                                         >  3:182103/1‑141 (MQ=255)                   tCACCCCGGGCCTGCGCCGCTTCGTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAAt                                                                                                                                         <  4:182103/141‑1 (MQ=255)                       cccGGGCCTGCGCCGCTTCGTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATc                                                                                                                             >  6:256979/1‑149 (MQ=255)                         cGGGCCTGCGCCGCTTCGTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCgg                                                                                                                           <  1:258427/149‑1 (MQ=255)                         cGGGCCTGCGCCGCTTCGTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCgg                                                                                                                           <  8:45275/149‑1 (MQ=255)                                gcgcCGCTTCGTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGcc                                                                                                                                              <  7:224124/123‑1 (MQ=255)                                gcgcCGCTTCGTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGcc                                                                                                                                              >  8:224124/1‑123 (MQ=255)                                   ccgcTTCGTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGatc                                                                                                                 <  3:235265/149‑1 (MQ=255)                                      cTTCGTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGatcatc                                                                                                              >  1:243010/1‑149 (MQ=255)                                       ttCGTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGAt                                                                                                                              <  8:85514/132‑1 (MQ=255)                                       ttCGTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGAt                                                                                                                              >  7:85514/1‑132 (MQ=255)                                          gTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCAATGCAGCCCCaa                                                                                                                                          <  5:220768/117‑1 (MQ=255)                                          gTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCAATGCAGCCCCaa                                                                                                                                          >  6:220768/1‑117 (MQ=255)                                             cgcAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCAATGCAGCCCCAAt                                                                                                                                         >  3:228852/1‑115 (MQ=255)                                             cgcAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCAATGCAGCCCCAAt                                                                                                                                         <  4:228852/115‑1 (MQ=255)                                                aaCGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAg                                                                                                        <  4:222440/145‑1 (MQ=255)                                                aaCGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGcag                                                                                                     >  3:222440/1‑146 (MQ=255)                                                    cTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAgg                                                                                                <  5:256979/149‑1 (MQ=255)                                                       gCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCtt                                                                                             >  2:212376/1‑149 (MQ=255)                                                           gCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGccc                                                                                         >  3:89048/1‑149 (MQ=255)                                                            ccGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGccc                                                                                         <  7:73772/148‑1 (MQ=255)                                                                   aGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGc                                                                                 <  2:29015/149‑1 (MQ=255)                                                                     ccACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTTTTTGATGGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGccc                                                                               >  4:21910/1‑149 (MQ=255)                                                                                ccAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCAccgcc                                                                       <  8:114847/146‑1 (MQ=255)                                                                                 cAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCga                                                                   <  2:243010/149‑1 (MQ=255)                                                                                 cAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATAATAGGGTAGCGATAAGGCTTGCCCACATACGCCCGCAACGCCGCga                                                                   >  6:36212/1‑149 (MQ=255)                                                                                        cACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCgatg‑atgat                                                           >  5:76424/1‑149 (MQ=255)                                                                                         aCCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAACAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCGATG‑ATGATc                                                          <  3:58065/149‑1 (MQ=255)                                                                                         aCCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCgatg‑atgat                                                           <  8:165570/148‑1 (MQ=255)                                                                                         aCCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAACGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCGATG‑ATGATc                                                          <  3:61695/149‑1 (MQ=255)                                                                                                   gtcgACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTATCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCGATG‑ATGATCAATatcatc                                                 <  7:12682/148‑1 (MQ=255)                                                                                                      gACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGgcc                                                                                                                         >  6:158119/1‑74 (MQ=255)                                                                                                      gACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGgcc                                                                                                                         <  5:158119/74‑1 (MQ=255)                                                                                                            gACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCGATG‑ATGATCAATATCATCACTGCCACCg                                       >  8:97349/1‑149 (MQ=255)                                                                                                             aCTGGACGCTTAACATCTAAAAGGCCATTGGGGCTGCATTGCATCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCGATG‑ATGATCAATATCATCACTGCCACCGt                                      <  5:36212/149‑1 (MQ=255)                                                                                                                 gACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATCTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCGATG‑ATGATCAATATCATCACTGCCACCGTGa                                    <  6:39417/147‑1 (MQ=255)                                                                                                                 gACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATCTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCGATG‑ATGATCAATATCATCACTGCCACCGTGa                                    >  5:39417/1‑147 (MQ=255)                                                                                                                      tGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCGATG‑ATGATCAATATCATCACTGCCACCGTGAGCATgg                              >  2:76688/1‑148 (MQ=255)                                                                                                                        aCCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCGATG‑ATGATCAATATCATCACTGCCACCGTGAGCATGGc                             <  6:76424/147‑1 (MQ=255)                                                                                                                          cATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCGATG‑ATGATCAATATCATCACTGCCACCGTGAGCATGGCAAAc                         <  7:97349/149‑1 (MQ=255)                                                                                                                                 aaGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCGATG‑ATGATCAATATCATCACTGCCACCGTGAGCATGGCAAACAGCACCa                  <  1:76688/149‑1 (MQ=255)                                                                                                                                  aGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCGATG‑ATGATCAATATCATCACTGCCACCGTGAGCATg                               >  7:33550/1‑135 (MQ=255)                                                                                                                                  aGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCGATG‑ATGATCAATATCATCACTGCCACCGTGAGCATg                               <  8:33550/135‑1 (MQ=255)                                                                                                                                      cATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCACGCACCGCCGCGATG‑ATGATCAATATCATCACTGCCACCGTGAGCATGGCAAACAGCACCAGccc              >  5:35242/1‑148 (MQ=255)                                                                                                                                      cATTGGGGCTGCAATGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCGATG‑ATGATCAATATCATCACTGCCACCGTGAGCATg                               >  7:247325/1‑131 (MQ=255)                                                                                                                                      cATTGGGGCTGCAATGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCGATG‑ATGATCAATATCATCACTGCCACCGTGAGCATg                               <  8:247325/131‑1 (MQ=255)                                                                                                                                              cTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCGATG‑ATGATCAATATCATCACTGCCACCGTGAGCATGGCAAACAGCACCAGCCCGATAAacac     >  6:104282/1‑149 (MQ=255)                                                                                                                                              cTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCGATG‑ATGATCAATATCATCACTGCCACCGTGAGCATGGCAAACAGCACCAGCCCGATAAacac     >  2:100044/1‑149 (MQ=255)                                                                                                                                                   ttGCATGCCCAATGGGTATTTTATCGGCCGCCAGTTCCTCGGGTATCGTTTAGGCTTGCCCTCATTGGGCCGGACCGCCGCGTTGTTTAATCAATATCATCACTGCCACCGTGAGCATGGCAAACAGCACCAGCCCGATAAACACGaa  <  1:212376/148‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                    GGTTCGACTACCAGATCCTCACCCCGGGCCTGCGCCGCTTCGTGCGCAACGCTCGCCTGCCGCGTCAGCCACGCTTCTCCCAGCATGCACCGCTGATCGTCGACTATGACTGGACGCTGACCATCTAAAAGGCCATTGGGGCTGCATTGCAGCCCCAATGGTTATTTGATCGGCCGCCAGATCATCGGGTAGCGATAAGGCTTGCCCTCATTCGCCCGCACCGCCGCGATG‑ATGATCAATATCATCACTGCCACCGTGAGCATGGCAAACAGCACCAGCCCGATAAACACGAA  >  NC_002947/6040648‑6040940

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: ‑