Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,056,958:1	+A	7.5%	coding (390/990 nt)	PP_2669 ←	outer membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,056,958	1	.	A	7.5%	203.7 / 12.0	53	coding (390/990 nt)	PP_2669	outer membrane protein
Reads supporting (aligned to +/- strand):  ref base . (26/23);  new base A (2/2);  total (28/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01

GGCCAGGGTCTGGGTGCTGGTGTCGATCCAGTGCAGCATGTTGGTGGTTTCGCTGGTGTTGACCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTTGATGATCTTGCGGGTGGCCACGTCCATCACCTGCACCCGGTCC  >  NC_002947/3056811‑3057105                                                                                                                                                     |                                                                                                                                                    ggCCAGGGTCTGGGTGCTGGTGTCGATCCAGTGCAGCATGTTGGTGGTTTCGCTGGTGTTGACCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGgtg                                                                                                                                                      <  6:378128/148‑1 (MQ=255)    cAGGGTCTGGGTGCTGGTGTCGATCCAGTGCAGCATGTTGGTGGTTTCGCTGGTGTTGACCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGa                                                                                                                                                 >  2:341434/1‑149 (MQ=255)         tCTGGGTGCTGGTGTCGATCCAGTGCAGCATGTTGGTGGTTTCGCTGGTGTTGACCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCAcc                                                                                                                                            >  7:146664/1‑149 (MQ=255)                         gATCCAGTGCAGCATGTTGGTGGTTTCGCTGGTGTTGACCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCAAGCACCTTGTCGGTGACGGTGATCGA‑CACCGTCAc                                                                                                                                       <  6:16413/138‑1 (MQ=255)                         gATCCAGTGCAGCATGTTGGTGGTTTCGCTGGTGTTGACCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTACGGGTTCGATGCCGACTTCGATCTGCCCAAGCACCTTGTCGGTGACGGTGATCGA‑CACCGTCAc                                                                                                                                       >  5:16413/1‑138 (MQ=255)                                        gTTGGTGGTTTCGCTGGTGTTGACCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGa                                                                                                                  >  3:59786/1‑144 (MQ=255)                                        gTTGGTGGTTTCGCTGGTGTTGACCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGa                                                                                                                  <  4:59786/144‑1 (MQ=255)                                         ttGGTGGTTTCGCTGGTGTTGACCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTcc                                                                                                                          <  6:131338/135‑1 (MQ=255)                                         ttGGTGGTTTCGCTGGTGTTGACCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTcc                                                                                                                          >  5:131338/1‑135 (MQ=255)                                           ggtggtTTCGCTGGTGTTGACCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGatacatac                                                                                                           <  1:341434/148‑1 (MQ=255)                                                         tgtTGACCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTg                                                                                            <  3:118613/149‑1 (MQ=255)                                                           ttGACCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTggg                                                                                          >  5:118556/1‑149 (MQ=255)                                                             gACCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGt                                                                                        >  2:68806/1‑149 (MQ=255)                                                              aCCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCTCCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGttt                                                                                                                    >  2:367100/1‑120 (MQ=255)                                                              aCCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCTCCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGttt                                                                                                                    <  1:367100/120‑1 (MQ=255)                                                              aCCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGAtacataca                                                                                                          <  6:374665/130‑1 (MQ=255)                                                              aCCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGAtacataca                                                                                                          >  5:374665/1‑130 (MQ=255)                                                              aCCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTg                                                                                       >  7:346738/1‑149 (MQ=255)                                                              aCCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTCCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTg                                                                                       >  6:105908/1‑149 (MQ=255)                                                                cGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTc                                                                                                                           >  4:376068/1‑111 (MQ=255)                                                                cGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTc                                                                                                                           <  3:376068/111‑1 (MQ=255)                                                                         gCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGaa                                                                              <  8:346738/147‑1 (MQ=255)                                                                         gCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAAc                                                                             <  3:324293/148‑1 (MQ=255)                                                                                          ccATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGt                                                                                                                      >  1:224256/1‑90 (MQ=255)                                                                                          ccATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGt                                                                                                                      <  2:224256/90‑1 (MQ=255)                                                                                          ccATGCCGTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCTTGGCGAACTGCTCGGGGTCCTTGCCg                                                           <  2:339410/149‑1 (MQ=255)                                                                                           cATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGGGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCgg                                                          <  3:98238/149‑1 (MQ=255)                                                                                                 ttCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGt                                                                                        >  3:126125/1‑113 (MQ=255)                                                                                                 ttCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGt                                                                                        <  4:126125/113‑1 (MQ=255)                                                                                                         cGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCtt                                             <  8:146664/148‑1 (MQ=255)                                                                                                          gATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTtg                                            <  6:118556/148‑1 (MQ=255)                                                                                                                   ttCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGGCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTTGATGATCTTGc                                  >  6:290688/1‑149 (MQ=255)                                                                                                                     cGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACt                                                 >  3:251400/1‑132 (MQ=255)                                                                                                                     cGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACt                                                 <  4:251400/132‑1 (MQ=255)                                                                                                                     cGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTtg                                            >  1:78305/1‑137 (MQ=255)                                                                                                                     cGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTtg                                            <  2:78305/137‑1 (MQ=255)                                                                                                                       aTCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATAcagccag                                                                                                     <  4:237324/78‑1 (MQ=255)                                                                                                                       aTCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATAcagccag                                                                                                     >  3:237324/1‑78 (MQ=255)                                                                                                                       aTCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTTGATGATCTTGCg                                 >  4:84957/1‑146 (MQ=255)                                                                                                                       aTCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTTGATGATCTTGCg                                 <  3:84957/146‑1 (MQ=255)                                                                                                                        tCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTg                                                                           >  4:57012/1‑103 (MQ=255)                                                                                                                        tCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTg                                                                           <  3:57012/103‑1 (MQ=255)                                                                                                                          tGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTTGATGATCTTGCGGGTGGc                           >  2:352823/1‑149 (MQ=255)                                                                                                                            cccGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTTGATGATCTTGCGGGTGGCCa                         >  2:57131/1‑149 (MQ=255)                                                                                                                            cccGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGACGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTTGATGATCTTGCGGGTGGcc                          <  1:194204/148‑1 (MQ=255)                                                                                                                                     cTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTTGATGATCTTGCGGGTGGCCACGTCCATCa                >  3:184017/1‑149 (MQ=255)                                                                                                                                         ctggTGACGGTGATCGA‑CACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTTGATGATCTTGCGGGTGGCCACGTCCATCACCt             <  4:330185/146‑1 (MQ=255)                                                                                                                                         ctggTGACGGTGATCGA‑CACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTTGATGATCTTGCGGGTGGCCACGTCCATCACCt             >  3:330185/3‑148 (MQ=255)                                                                                                                                          cGGTGCCGGGG‑GCGATCACCGTCACCAGCGCAGCGGCCTCGTCTGCTACATACAGCCAGCGGGCGTTGGGGTGCAGCGCGAACTGCTCGGGGTCCTCGCCGGAAGGCAACTCCTTGATGATCTTGCGGGTGGCCACGTCCATCACCTGc           <  4:269190/149‑1 (MQ=255)                                                                                                                                          cGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTTGATGATCTTGCGGGTGGCCACGTCCATCACCTg            >  2:138996/1‑148 (MQ=255)                                                                                                                                          cGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTTGATGATCTTGCGGGTGGCCACGTCCATCACCTg            >  2:133758/1‑148 (MQ=255)                                                                                                                                            gTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTTGATGATCTTGCGGGTGGCCACGTCCATCACCTGCAc         >  2:348196/1‑149 (MQ=255)                                                                                                                                             tGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTTGATGATCTTGCGGGTGGCCACGTCCATCACCTGCAcc        >  3:169656/1‑149 (MQ=255)                                                                                                                                                cGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTTGATGATCTTGCGGGTGGCCACGTCCATCACCTGCACCCgg     <  4:184017/149‑1 (MQ=255)                                                                                                                                                  gtg‑tCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTTGATGATCTTGCGGGTGGCCACGTCCATCACCTGCACCCGGTc   <  1:68806/149‑1 (MQ=255)                                                                                                                                                   tg‑tCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTTGATGATCTTGCGGGTGGCCACGTCCATCACCTGCACCCGGTcc  <  5:105908/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                    GGCCAGGGTCTGGGTGCTGGTGTCGATCCAGTGCAGCATGTTGGTGGTTTCGCTGGTGTTGACCGCCCACTTGCCGTCGGGGCTGACCGCCATGCCTTCGGGTTCGATGCCGACTTCGATCTGCCCGAGCACCTTGTCGGTGACGGTG‑TCGATCACCGTCACCAGCGCATCGTCCTCGTTTGATACATACAGCCAGCGGTCGTTGGGGTGCAGGGCGAACTGCTCGGGGTCCTTGCCGGAAGGCAACTCCTTGATGATCTTGCGGGTGGCCACGTCCATCACCTGCACCCGGTCC  >  NC_002947/3056811‑3057105

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: ‑