Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,789,421	T→C	7.5%	V193A (GTC→GCC)	ynfM →	efflux transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,789,421	0	T	C	7.5%	147.4 / 2.3	53	V193A (GTC→GCC)	ynfM	efflux transporter
Reads supporting (aligned to +/- strand):  ref base T (22/27);  new base C (2/2);  total (24/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.60e-01

CTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACATTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTCCGCGCACAGACGATGAACCCACGCAGCCTGCTGGACGGCTTTGTCATGCA  >  NC_002947/5789273‑5789562                                                                                                                                                     |                                                                                                                                              cTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACATTGGCCTGGCCATGGGCCTGTACATCGTCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGt                                                                                                                                               <  6:104217/149‑1 (MQ=255)        gCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACATTGGCCTGGTCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTgg                                                                                                                                        >  5:256396/1‑149 (MQ=255)        gCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACATTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTgg                                                                                                                                        <  5:106061/149‑1 (MQ=255)          cTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACATTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGca                                                                                                                                      <  2:92712/149‑1 (MQ=255)                gcAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACATTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGc                                                                                                                                <  7:333594/149‑1 (MQ=255)                    tGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACATTGGCCTGGTCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATg                                                                                                                            <  6:256396/149‑1 (MQ=255)                       cGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACATTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCt                                                                                                                          >  1:97512/1‑148 (MQ=255)                                aCCTGAGCGAAGAGATCCACCCGCAACACATTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGt                                                                                                                                               <  3:267023/118‑1 (MQ=255)                                aCCTGAGCGAAGAGATCCACCCGCAACACATTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGt                                                                                                                                               >  4:267023/1‑118 (MQ=255)                                  cTGAGCGAAGAGATCCACCCGCAACACATTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTggcgg                                                                                                              >  8:207583/1‑149 (MQ=255)                                  cTGAGCGAAGAGATCCACCCGCAACACATTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTggcgg                                                                                                              >  6:234603/1‑149 (MQ=255)                                         aaGAGATCCACCCGCAACACATTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGcc                                                                                                       <  7:47287/149‑1 (MQ=255)                                              aTCCACCCGCAACACATTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCtggt                                                                                                  <  7:207583/149‑1 (MQ=255)                                                ccACCCGCAACACATTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCtggtgg                                                                                                >  1:317447/1‑149 (MQ=255)                                                   cccGCAACACATTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGAGGCCTGGCCCTGGTGGCcg                                                                                             >  6:203374/1‑149 (MQ=255)                                                    ccGCAACACATTGGCCTGGCCATGGGCCTGTACATCGGGGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGTTGGCcgc                                                                                            <  2:97512/149‑1 (MQ=255)                                                         acacATTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCcg                                                                                             >  3:124251/1‑143 (MQ=255)                                                         acacATTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCcg                                                                                             <  4:124251/143‑1 (MQ=255)                                                         acacATTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTgg                                                                                       >  8:240602/1‑149 (MQ=255)                                                           acaTTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTa                                                                                     >  3:238393/1‑149 (MQ=255)                                                                ggcctggccATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTg                                                                                >  5:118075/1‑149 (MQ=255)                                                                    tggccATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAg                                                                            >  6:256691/1‑149 (MQ=255)                                                                    tggccATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAg                                                                            >  2:165774/1‑149 (MQ=255)                                                                        cATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCAATGCCGCCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGtga                                                                        >  8:254898/1‑148 (MQ=255)                                                                            ggCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGtgctgc                                                                     <  5:234603/148‑1 (MQ=255)                                                                            ggCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGcc                                                                    <  7:120802/149‑1 (MQ=255)                                                                               cTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGa                                                                 <  1:165774/149‑1 (MQ=255)                                                                                 gTACATCGGCGGAAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGACCTGGTGGACGCGCTGGTATTCTGGAAGGTGATGCCGGAGt                                                               >  6:331320/1‑149 (MQ=255)                                                                                  tACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGGACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGt                                                               <  8:245553/148‑1 (MQ=255)                                                                                     aTCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACg                                                           >  6:105764/1‑149 (MQ=255)                                                                                            tcAACGCGATTGGCGGCATGAGCGGGCGTATCATCACGGGCGTACTGATCGACTTCGTCAGCTTGCACAAGGCGATGCTGACCATTGGCGGCCTGGCCCTGTTGGCCGCGCTGGTATTCTGGAAGGTTCTGCCGGAGTCACGCAATTTc                                                    <  5:331320/148‑1 (MQ=255)                                                                                            gcAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTc                                                    <  6:118075/149‑1 (MQ=255)                                                                                             cAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTcc                                                   <  7:35901/149‑1 (MQ=255)                                                                                             cAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTcc                                                   <  7:240602/149‑1 (MQ=255)                                                                                                 gcgATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCcg                                                                                             <  5:70326/103‑1 (MQ=255)                                                                                                 gcgATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCcg                                                                                             >  6:70326/1‑103 (MQ=255)                                                                                                 gcgATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTCcgc                                                 <  1:151210/147‑1 (MQ=255)                                                                                                 gcgATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTCcgc                                                 >  2:151210/1‑147 (MQ=255)                                                                                                     ttGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTCCGCGCACAg                                           <  5:105764/149‑1 (MQ=255)                                                                                                                   gggCGTCTCATCACGGGCGTACTGATCGACTTCGCCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTCCGCGCACAGACGATGAACCCACg                             >  6:133445/1‑149 (MQ=255)                                                                                                                   gggCGTCTCATCACGGGCGTACTGATCGACTTCGCCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTCCGCGCACAGACGATGAACCCACg                             >  6:127808/1‑149 (MQ=255)                                                                                                                     gCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGACTGGCCCTGGTGGCAGCGCTGGTATTCTGGAAGGTCCTGCCGGAGTCACGCAATTTCCGCGCACAGACGATGAACCCCCg                             >  5:358602/1‑147 (MQ=255)                                                                                                                       gTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTCCGCGCACAGACGATGAACCCACGCAGc                         <  3:19207/149‑1 (MQ=255)                                                                                                                            atcaCGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTCCGCGCACAGACGATGAACCCACGCAGCctgct                    >  1:306931/1‑149 (MQ=255)                                                                                                                             tcaCGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTCCGCGCACAGACGATGAACCCACGCAGCctgctg                   <  5:256691/149‑1 (MQ=255)                                                                                                                                    cGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTCCGCGCACAGACGATGAACCCACGCAGCCTGCTGGACGGCt            <  7:254898/149‑1 (MQ=255)                                                                                                                                      tACTGATCGACTTGGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGATGGTGCTGCCGGAGTCACGCAATTTCCGCGCACAGACGATGAACCCACGCAGCCTGCTGGACGGCttt          <  4:238393/149‑1 (MQ=255)                                                                                                                                       aCTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTCCGCGCACAGACGATGAACCCACGCAGCCTGCTGGACGGCTTTg         >  6:367399/1‑149 (MQ=255)                                                                                                                                           aTCGACTTCGCCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTCCGCGCACAGACGATGAACCCACGCAGCCTGCTGGACGGCTTTGTc       <  5:127808/147‑1 (MQ=255)                                                                                                                                           aTCGACTTCGCCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTCCGCGCACAGACGATGAACCCACGCAGCCTGCTGGACGGCTTTGTc       <  5:133445/147‑1 (MQ=255)                                                                                                                                            tCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTCCGCGCACAGACGATGAACCCACGCAGCCTGCTGGACGGCTTTGTCATg    <  5:367399/149‑1 (MQ=255)                                                                                                                                              gACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTCCGCGCACAGACGATGAACCCACGCAGCCTGCTGGACGGCTTTGTCATGCa  <  2:306931/149‑1 (MQ=255)                                                                                                                                               aCTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGc                                                          <  3:326276/92‑1 (MQ=255)                                                                                                                                               aCTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGc                                                          >  4:326276/1‑92 (MQ=255)                                                                                                                                               aCTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTCCGCGCACAGACGATGAACCCAc                              >  6:111287/1‑120 (MQ=255)                                                                                                                                               aCTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTCCGCGCACAGACGATGAACCCAc                              <  5:111287/120‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                              CTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACATTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCATGAGCGGGCGTCTCATCACGGGCGTACTGATCGACTTCGTCAGCTGGCACACGGCGATGCTGACCATTGGCGGCCTGGCCCTGGTGGCCGCGCTGGTATTCTGGAAGGTGCTGCCGGAGTCACGCAATTTCCGCGCACAGACGATGAACCCACGCAGCCTGCTGGACGGCTTTGTCATGCA  >  NC_002947/5789273‑5789562

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: ‑