Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,790,014	T→C	8.3%	W391R (TGG→CGG)	ynfM →	efflux transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,790,014	0	T	C	8.3%	129.1 / 2.8	48	W391R (TGG→CGG)	ynfM	efflux transporter
Reads supporting (aligned to +/- strand):  ref base T (17/27);  new base C (2/2);  total (19/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.36e-01

TTCACCTTCGGCTTCTTTGGTGCGCACTCGGTGGCCAGCAGCTGGATCGGCCGCCGGGCGCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTGGCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGT  >  NC_002947/5789867‑5790155                                                                                                                                                      |                                                                                                                                              ttCACCTTCGACTTCTTTGGTGCGCACTCGGTGGCCAGCAGCTGGATCGGCCGCCGGGCGCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTg                                                                                                                                              >  6:156559/1‑149 (MQ=255)    aCCTTCGGCTTCTTGGGTGCGCACGCGGGGGCCAGCAGCTGGAGCGGCCGCCGGGCGCTGAAGGCCAAGGGGCAGGCGTCGGCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCa                                                                                                                                           <  4:131153/149‑1 (MQ=255)     ccTTCGGCTTCTTTGGTGCGCACTCGGTGGCCAGCAGCTGGATCGGCCGCCGGGCGCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCAc                                                                                                                                          <  6:118943/149‑1 (MQ=255)      cTTCGGCTTCTTTGGTGCGCACTCGGTGGCCAGCAGCTGGATCGGCCGCCGGGCGCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCAc                                                                                                                                          >  7:40759/1‑148 (MQ=255)               cttTGGTGCGCACTCGGTGGCCAGCAGCTGGATCGGCCGCCGGGCGCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTgggg                                                                                                                                  <  2:308431/147‑1 (MQ=255)                  tGGTGCGCACTCGGTGGCCAGCAGCTGGATCGGCCGCCGGGCGCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCt                                                                                                                                <  8:278706/146‑1 (MQ=255)                     tGCGCACTCGGTGGCCAGCAGCTGGATCGGCCGCCGGGCGCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGGTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACg                                                                                                                          <  1:103732/149‑1 (MQ=255)                       cgcACTCGGTGGCCAGCAGCTGGATCGGCCGCCGGGCGCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACgg                                                                                                                         <  5:156559/148‑1 (MQ=255)                       cgcACTCGGTGGCCAGCAGCTGGATCGGCCGCCGGGCGCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCCAGCCCCACTGGTGCCAGAAcacc                                                                                                                        <  1:151156/149‑4 (MQ=255)                         cACTCGGTGGCCAGCAGCTGGATCGGCCGCCGGGCGCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTTCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGAt                                                                                                                      <  1:358141/149‑1 (MQ=255)                          aCTCGGTGGCCAGCAGCTGGATCGGCCGCCGGGCGCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATc                                                                                                                     <  8:40759/149‑1 (MQ=255)                           cTCGGTGTCCAGCAGCTGGATCGGCCGCCGGGCGCTGACGGCCACGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCGGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCg                                                                                                                    <  6:113670/149‑1 (MQ=255)                           cTCGGTGGCCAGCAGCAGGATCGGCCGCCGGGCGCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCCAGCCCCACTGGTGccagaa                                                                                                                            >  4:195093/1‑136 (MQ=255)                           cTCGGTGGCCAGCAGCAGGATCGGCCGCCGGGCGCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCCAGCCCCACTGGTGccagaa                                                                                                                            <  3:195093/141‑6 (MQ=255)                            tCGGTGGCCAGCAGCTGGATCGGCCGCCGGGCGCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCgg                                                                                                                   >  6:233923/1‑149 (MQ=255)                              ggTGGCCAGCAGCTGGATCGGCCGCCGGGCTCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGGTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCt                                                                                                                                <  6:132307/134‑1 (MQ=255)                              ggTGGCCAGCAGCTGGATCGGCCGCCGGGCGCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCggg                                                                                                                  <  5:369206/148‑1 (MQ=255)                              ggTGGCCAGCAGCTGGATCGGCCGCCGGGCCCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCt                                                                                                                                >  5:132307/1‑134 (MQ=255)                                      gcagcTGGATCGGCCGCCGGGCGCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCAtt                                                                                                         >  3:297298/1‑149 (MQ=255)                                          cTGGATCGGCCGCCGGGCGCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTgg                                                                                                       >  3:170157/1‑147 (MQ=255)                                                  gccgccGGGCGCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTg                                                                                             >  4:227100/1‑149 (MQ=255)                                                      ccgGGCGCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCgg                                                                                         <  3:227100/149‑1 (MQ=255)                                                           cgcTGAAGGCCAAGGGGCAGGCGTCGGCGCTGTACCTGTTCTGCTACTACGCTGGGTCCAGCGTGGCCGGTACGGCGGGCCTCGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTgg                                                                                      <  1:287593/149‑1 (MQ=255)                                                              tGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCtt                                                                                  >  4:322622/1‑148 (MQ=255)                                                                aaGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGAt                                                                               <  1:259673/149‑1 (MQ=255)                                                                  ggCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGATCGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGt                                                                                        <  2:252080/138‑1 (MQ=255)                                                                  ggCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGt                                                                                        <  7:106638/138‑1 (MQ=255)                                                                  ggCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGt                                                                                        >  1:252080/1‑138 (MQ=255)                                                                  ggCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGt                                                                                        >  8:106638/1‑138 (MQ=255)                                                                    ccAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGAtggtg                                                                           <  2:355336/149‑1 (MQ=255)                                                                     cAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTgg                                                                                                       >  7:18372/1‑120 (MQ=255)                                                                     cAAGGGGCAGGCGGCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTgg                                                                                                       <  8:18372/120‑1 (MQ=255)                                                                             aGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTGGCGTTGCAc                                                                  >  1:131904/1‑149 (MQ=255)                                                                               gCGTCGTCGCTGTACCTGTTCTGCTACTTCGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTGGCGTTGCACCt                                                                >  1:201212/1‑149 (MQ=255)                                                                               gCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTGGCGTTGCACCt                                                                <  5:19695/149‑1 (MQ=255)                                                                                    gtcgCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTGGCGTTGCACCTGAGc                                                            >  4:154694/1‑148 (MQ=255)                                                                                        cTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTGGCGt                                                                       >  2:203932/1‑133 (MQ=255)                                                                                             ccTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTGGCGTTGCACCTGAGCAAGTTGCCa                                                   <  4:170157/148‑1 (MQ=255)                                                                                             ccTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTGGCGTTGCACCTGAGCAAGTTGCCAc                                                  <  4:297298/149‑1 (MQ=255)                                                                                                        actacGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCCGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGAGGCCTTGATGGTGGCGTTGCACCTGAGCAAGTTGCCACCCAACACGgtg                                       >  4:303479/1‑149 (MQ=255)                                                                                                         ctacGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTGGCGTTGCACCTGAGCAAGTTGTCACCCAAAACGgt                                        <  3:154694/147‑1 (MQ=255)                                                                                                         ctacGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTGGCGTTGCACCTGAGCAAGTTGCCACCCAAAACGgt                                        <  3:340380/147‑1 (MQ=255)                                                                                                              cTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTGGCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATg                                  >  7:247691/1‑148 (MQ=255)                                                                                                                     cAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTGGCGt                                                                       >  2:148667/1‑104 (MQ=255)                                                                                                                     cAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTGGCGt                                                                       <  1:148667/104‑1 (MQ=255)                                                                                                                      aGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTGGCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTgg                         <  2:201212/149‑1 (MQ=255)                                                                                                                      aGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTGGCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTgg                         <  8:247691/149‑1 (MQ=255)                                                                                                                                               ggTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTGGCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCtgt  <  5:233923/149‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                              TTCACCTTCGGCTTCTTTGGTGCGCACTCGGTGGCCAGCAGCTGGATCGGCCGCCGGGCGCTGAAGGCCAAGGGGCAGGCGTCGTCGCTGTACCTGTTCTGCTACTACGCTGGCTCCAGCGTGGCCGGTACGGCGGGC‑‑GGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTGGCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGT  >  NC_002947/5789867‑5790155

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: ‑