Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,612,669	A→C	6.8%	intergenic (+1631/‑476)	hcpC‑II → / → PP_4084	hemolysin‑coregulated protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,612,669	0	A	C	6.8%	174.7 / 2.2	56	intergenic (+1631/‑476)	hcpC‑II/PP_4084	hemolysin‑coregulated protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (24/28);  new base C (2/2);  total (26/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGGGCGCACTTACTGCGGTGACCAACTGCCGCCTTACGATCTGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCAGGACGAATCGGTCGCCATTGGCCGCAATCGTCTGCGCGTCGTCAAGGCCAACGACACCTTGAA  >  NC_002947/4612523‑4612817                                                                                                                                                    |                                                                                                                                                     ccGGGCGCACTTACTGCGGTGACCAACTGCCGCCTTACGATCTGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGAAAGGAGGAAG‑TGTTCAt                                                                                                                                                     >  3:242276/1‑148 (MQ=255)       gcACTTACTGCGGTGACCAACTGCCGCCTTACGATCTGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGcc                                                                                                                                              <  6:233586/149‑1 (MQ=255)         aCTTACTGCGGTGACCAACTGCCGCCTTACGATCTGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGcc                                                                                                                                              >  2:49586/1‑147 (MQ=255)           ttACTGCGGTGACCAACTGCCGCCTTACGATCTGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCa                                                                                                                                            >  7:133715/1‑147 (MQ=255)             aCTGCGGTGACCAACTGCCGCCTTACGATCTGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCATAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCaga                                                                                                                                          <  1:194706/147‑1 (MQ=255)             aCTGCGGTGACCAACTGCCGCCTTACGATCTGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCaga                                                                                                                                          <  7:229001/147‑1 (MQ=255)              cTGCGGTGACCAACTGCCGCCTTACGATCTGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCaga                                                                                                                                          >  2:145944/1‑146 (MQ=255)                 cGGTGACCAACTGCCGCCTTACGATCTGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCATGGATGAAC‑ACTTCCTCCTTGCCCagctcat                                                                                                                                      <  2:17230/147‑6 (MQ=21)                    tGACCAACTGCCGCCTTACGATCTGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAg                                                                                                                                  >  4:149101/1‑148 (MQ=255)                           cTGCCGCCTTACGATCTGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACActct                                                                                                                          >  2:94686/1‑149 (MQ=255)                           cTGCCGCCGTTCGATCTGCCCGATCACAAAACACGCATTACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACActct                                                                                                                          <  8:133715/149‑1 (MQ=255)                              ccgccTTACGATCTGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAGCTGTTCATCCATGCCCAGAGAGATCAGAACACTCTg                                                                                                                         <  1:49586/148‑1 (MQ=255)                              ccgccTTACGATCTGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTg                                                                                                                         <  6:261261/147‑1 (MQ=255)                              ccgccTTACGATCTGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATACCCAGAGAGATCAGAACACTCTg                                                                                                                         <  7:509/147‑1 (MQ=255)                               cgccTTACGATCTGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGt                                                                                                                       >  4:22310/1‑148 (MQ=255)                               cgccTTACGATCTGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGt                                                                                                                       <  3:22310/148‑1 (MQ=255)                                 ccTTACGATCTGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCa                                                                                                                     >  1:157724/1‑148 (MQ=255)                                 ccTTACGATCTGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCa                                                                                                                     <  2:157724/148‑1 (MQ=255)                                       gATCTGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACaa                                                                                                              >  1:165324/1‑149 (MQ=255)                                           tGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAg                                                                                                          >  7:302415/1‑149 (MQ=255)                                            gCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAAt                                                                                                                   <  7:128898/139‑1 (MQ=255)                                            gCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAAt                                                                                                                   >  8:128898/1‑139 (MQ=255)                                             ccagATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACaa                                                                                                              <  1:145944/140‑1 (MQ=255)                                                  tCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCctct                                                                                                   <  2:165324/149‑1 (MQ=255)                                                    acaAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCctctct                                                                                                 >  2:324107/1‑149 (MQ=255)                                                     caAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAAc                                                                                                             <  7:262539/136‑1 (MQ=255)                                                     caAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAAc                                                                                                             >  8:262539/1‑136 (MQ=255)                                                      aaaaCACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCtgt                                                                                               >  6:13597/1‑149 (MQ=255)                                                          cacGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGc                                                                                           <  1:324107/149‑1 (MQ=255)                                                           acGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGt                                                                                                                       <  1:96184/120‑1 (MQ=255)                                                           acGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGt                                                                                                                       >  2:96184/1‑120 (MQ=255)                                                                    cATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCa                                                                                 <  5:13597/149‑1 (MQ=255)                                                                      tCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCAcc                                                                               >  4:83383/1‑149 (MQ=255)                                                                         agagCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCaa                                                                            <  4:242276/149‑1 (MQ=255)                                                                             ccAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCagaga                                                                                                                                        <  5:126850/85‑1 (MQ=255)                                                                             ccAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCagaga                                                                                                                                        >  6:126850/1‑85 (MQ=255)                                                                               aGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGtt                                                                      <  3:149101/149‑1 (MQ=255)                                                                                     acaAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCAg                                                                >  4:288744/1‑149 (MQ=255)                                                                                            ggAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCTCCCAACAGGTTGGCCAGGACGAAt                                                         <  8:302415/149‑1 (MQ=255)                                                                                                       aCGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCAGGACGAATCGGTCGCCAtt                                              >  3:159026/1‑149 (MQ=255)                                                                                                         gAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCAGGACGAATCGGTCGCCATTgg                                            <  3:288744/149‑1 (MQ=255)                                                                                                             tGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCAGGACGAATCGGTCGCCATTGGCCg                                         >  8:15737/1‑148 (MQ=255)                                                                                                                   tCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCAGGACGAATCGGTCGCCAtt                                              >  6:335827/1‑137 (MQ=255)                                                                                                                   tCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCAGGACGAATCGGTCGCCAtt                                              <  5:335827/137‑1 (MQ=255)                                                                                                                    cGAGGATGAGCTGGGCAAGGAGGAAG‑TGCTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACCACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCAGGACGAATCGGTCGCCATTGGCCGCAATCGt                                  <  6:192024/148‑1 (MQ=255)                                                                                                                         tctctcTGGGCATGGATGAAC‑ACTTCCTCCTTGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCAGGAc                                                             <  7:110922/111‑1 (MQ=25)                                                                                                                         tctctcTGGGCATGGATGAAC‑ACTTCCTCCTTGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCAGGAc                                                             >  8:110922/6‑116 (MQ=25)                                                                                                                           gAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCAGGACGAATCGGTCGCCATTGGCCGCAATCGTCTGCGcgt                          >  7:3703/1‑149 (MQ=255)                                                                                                                            ctcTGGGCATGGATGAAC‑ACTTCCTCCTTGCCCAGAGTGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCAGGACGAATCGGTCGCCATTGGCCGCAATCGTCTGCGcgtc                         >  1:58300/3‑149 (MQ=38)                                                                                                                             gCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCTGGACGAATCGGTCGCCATTGGCCGCAATCGTCTgcgc                            >  5:282077/1‑145 (MQ=255)                                                                                                                             gCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCAGGACGAATCGGTCGCCATTGGCCGCAATCGTCTgcgc                            <  6:282077/145‑1 (MQ=255)                                                                                                                                      ggaggaAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCAGGACGAATCGGTCGCCATTGGCCGCAATCGTCTGCGCGTCGTCaa                    <  6:295193/144‑1 (MQ=255)                                                                                                                                      ggaggaAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCAGGACGAATCGGTCGCCATTGGCCGCAATCGTCTGCGCGTCGTCaa                    >  5:295193/1‑144 (MQ=255)                                                                                                                                        aggaAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCAGGACGAATCGGTCGCCATTGGCCGCAATCGTCTGCGCGTCGTCAAGGCCAAc             <  3:83383/149‑1 (MQ=255)                                                                                                                                             g‑tgtTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCAGGACGAATCGGTCGCCATTGGCCGCAATCGTCTGCGCGTCGTCAAGGCCAACGacac        <  8:3703/149‑1 (MQ=255)                                                                                                                                                 ttCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCAGGACGAATCGGTCGCCATTGGCCGCAATCGTCTGCGCGTCGTCAAGGCCAACGACACCtt     <  4:159026/149‑1 (MQ=255)                                                                                                                                                    aTCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCAGGACGAATCGGTCGCCATTGGCCGCAATCGTCTGCGCGTCGTCAAGGCCAACGACACCTTGaa  <  5:115416/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                     CCGGGCGCACTTACTGCGGTGACCAACTGCCGCCTTACGATCTGCCCGATCACAAAACACGCATGACCATCAAGAGCCAGACCCACAAGGGGGAAGGTTTCAACGAGCTGCGTTTCGAGGATGAGCTGGGCAAGGAGGAAG‑TGTTCATCCATGCCCAGAGAGATCAGAACACTCTGGTCAATCACAACCAGTCCCTCTCTGTGGGCGTCGATCGCACCCAACAGGTTGGCCAGGACGAATCGGTCGCCATTGGCCGCAATCGTCTGCGCGTCGTCAAGGCCAACGACACCTTGAA  >  NC_002947/4612523‑4612817

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑