Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,717,014	0	T	G	44.0%	76.5 / 14.0	51	G156G (GGT→GGG)	yiaD	multicopy suppressor of bamB; outer membrane lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (6/22);  new base G (22/0);  total (29/22)
Fisher's exact test for biased strand distribution p-value = 5.24e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AATATGCCGAACAATGTGACCTTCGACAGCAGCAGCGCGACCCTGAAACCGGCGGGCGCTAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAACGTGA‑TTGGTTATACCGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGCCGCATCCGTACTCAGGGCCTTGGCCCGGCTAACCCAATCGCCAGCAACAGCACCGCAGAAGGTA  >  NC_000913/3716871‑3717162                                                                                                                                                 |                                                                                                                                                     aaTATGCCGAACAATGTGACCTTCGACAGCAGCAGCGCGACCCTGAAACCGGCGGGCCCTAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAACGTGA‑TTGGTTATACCGACAGCACGGGTGGTCACg                                                                                                                                               <  1:839594/151‑1 (MQ=255)         gtaCAATGTGACCTTCGACAGCAGCAGCGCGACCCTGAAACCGGCGGGCGCTAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGGTTAAGCGG‑TTTGGTATATCCACCGCACGGGGGGTcgaccactg                                                                                                                                          >  1:445292/3‑140 (MQ=255)             aaTGTGACCTTCGACAGCAGCAGCGCGACCCTGAAACCGGCGGGCGCTAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGGTAACAAGT‑CTGGATATACCCTCAACACTGGCGGTGACAACCtcgacacc                                                                                                                                    >  1:240964/1‑143 (MQ=255)                       tCGACAGCAGCAGCGCGACCCTGAAACCGGCGGGCGCTAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGGTTAAGGGA‑TTTGGTTTACCCGCAGCACCGGGGGGCACCGCCCGAAAAAGCGtccctccc                                                                                                                          >  2:5720/1‑150 (MQ=255)                        cGACAGCAGCAGCGCGACCCTGAAACCGGCGGGCGCTAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAACGTGA‑TTGGTTATACCGACAGTACGGGTGGTCACGACCTGAACATGCGTCTCTCCCa                                                                                                                         <  1:971799/150‑1 (MQ=255)                         gACAGCAGCAGCGCGACCCTGAAACCGGCGGGCGCTAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAACGTGA‑TTGGTTATACCGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGc                                                                                                                       <  1:953813/151‑1 (MQ=255)                          aCAGCAGCAGCGCGACCCTGAAACCGGCGGGCGCTAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAAAGTGA‑TTGGTTATACCGACAGCACGGGGGGTCACGACCTGAACATGCGTCTCTccc                                                                                                                          >  2:791534/1‑147 (MQ=255)                            agcagcagcGCGACCCTGAAACCGGCGGGCGCTAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAAAGGGG‑TTGGGTATAACCACAGCACGGGGGGGGCCCACCTTAACAAGCGTCTCTccccacca                                                                                                                     >  2:962189/1‑145 (MQ=255)                             gcagcagcGCGACCCTGAAACCGGCGGGCGCTAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAACGTGA‑TTGGTTATACCGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACg                                                                                                                   <  1:250506/151‑1 (MQ=255)                               agcagcGCGACCCTGAAACCGGCGGGCGCTAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAACGTGA‑TTTGGTATACCGACAGCACCGGGGGGCACGACCCGAACAAGCGTCTCTCCCCGCAAAGTg                                                                                                                 >  2:811155/1‑151 (MQ=255)                               agcagcGCGACCCTGAAACCGGCGGGCGCTAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGGTAACGTGATTTGGTTCAACCGA‑AGCACGGGGGGGCACAGCCCGAACCAACCTCTCTCCCCGCAACGTg                                                                                                                 >  2:973366/1‑151 (MQ=255)                                     gcgACCCTGAAACCGGCGGGCGCTAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAACGTGA‑TTGGTTATACCGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGAt                                                                                                            <  1:777299/150‑1 (MQ=255)                                       gACCCTGAAACCGGCGGGCGCTAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTTACGGGG‑TTTGGTTTAACGAAAGCACGGGGGGTTACCACCTGAAAATGCGTCTCTCCCCACCACGTGCGGGtttc                                                                                                         >  2:737283/1‑149 (MQ=255)                                       gACCCTGAAACCGGCGGGCGCTAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGGTTAAGTGG‑TTGGTTTTAACGACAGCACCGGGGGGGACGACCCGAAAAAGCGTCTCTCCCCCCCACGCGCggggttc                                                                                                         >  1:838973/1‑146 (MQ=255)                                          ccTGAAACCGGCGGGCGCTAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAACGTGA‑TTGGTTATACCGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGtt                                                                                                      <  1:441758/151‑1 (MQ=255)                                          ccTGAAACCGGCGGGCGCTAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGGTAACATGA‑TTGGTTATAACCACAACCCGGGGGGGCACCGCCTGTACAAGCGCCTCTCCCCCCAACGGGccg                                                                                                              >  2:135437/1‑141 (MQ=255)                                                 ccGGCGGGCGCTAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGGTAACGTGA‑TTGGTTATACCGACAGCACGGGGGGTCACGACCCGAACATGCGGCTCTCCCCGCAACGTGCGGATTCCGTTGCCAgc                                                                                                >  1:749562/1‑150 (MQ=255)                                                         cgcTAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAACGTGA‑TTGGTTATACCGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATc                                                                                       <  1:489207/151‑1 (MQ=255)                                                            tAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAACGGGA‑TTGGGTTTACCGACAGCACGGGGGGTCACGACCCGAACATGCGTCTCTCCCCGCAACGTGCGGGTTCCGTTGCCAGCGCGTTGGTCAcc                                                                                    >  1:167918/1‑151 (MQ=255)                                                               cacCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAACGTGA‑TTGGTTATACCGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAg                                                                                 <  2:216676/151‑1 (MQ=255)                                                                 cccTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAACGTGA‑TTGGTTATACCGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAgg                                                                                <  2:30105/150‑1 (MQ=255)                                                                   cTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAAAGTGA‑TTGGGTATAACGACAGCACGGGGGGGCACGACCTGAACATGCGTCTCTCCCCGCAACGTGCGGAATCCGTTGCCCGCGCGGTGATCACCCAGGGCg                                                                             >  2:471902/1‑151 (MQ=255)                                                                        cGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAACGTGA‑TTGGTTATACCGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGAc                                                                        <  2:851474/151‑1 (MQ=255)                                                                         ggCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTTACGTGA‑TTGGGTTTAACGACAGCACGGGGGGTCACGACCCGAACATGCGTCTCTCCCAGCAAAGTGCGGGTTCCCTTTCCAGCGCGTTGATCACCCCCGGCgggg                                                                          >  1:367960/1‑148 (MQ=255)                                                                           cGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAACGTGG‑TTGGTTATACCGACAGCACGGGGGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTgggc                                                                        >  2:114655/1‑146 (MQ=255)                                                                           cGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAACGTGA‑TTGGTTATACCGACAGCACGGGGGGGCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGGCGcc                                                                     >  2:105775/1‑151 (MQ=255)                                                                           cGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGGTAACGTGA‑TTGGTTATACCGACAGCACGGGGGGTCAAGACCCGGAAATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCCGCGCGGTGATCACCCAGGGCGTGGACGcc                                                                     >  1:33845/1‑151 (MQ=255)                                                                            gTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAACGTGG‑TTGGTTATACCGACAGCACGGGGGGTCACGACCCTAACATGCGTCTCTCCCAGCAAAGCGCGGATTCCGTTGCCAGCGCGGTGATCACCCAAGGCGTGGACGcc                                                                     >  1:778388/1‑150 (MQ=255)                                                                            gTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAAAGTGA‑TTGGTTATACCGACAGCACGGGTGGGGACGACCTGAAAATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGGTGGTCACCCAGGGCGGGGACGc                                                                      >  2:342996/1‑149 (MQ=255)                                                                               gCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAACGTGA‑TTGGTTATAACGACAGCACGGGGGGGCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGcc                                                                 >  2:37733/1‑151 (MQ=255)                                                                                cAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAACGTGA‑TTGGTTTTACCGACAGCACGGGGGGTCACGACCCGAACATGCGTCTCTCCCCGCAACGCGCGGGTTCCGTTGCCCGCGCGTTGATCACCCACGGCGTGGGCGCCAGcc                                                                 >  1:525757/1‑150 (MQ=255)                                                                                  aTGGTACTGAAAGAGTATCCGAAAACGGCGGTTAAAGTGA‑TTGGGTATACCGACAACACGGGGGGTCACGACCTGGAAAAGCGTCTCTCCCAGCCAAGTGCGGGTTCCCTTGCCCGCGCGGTGATCACCCCGGGCGGGGAcgcccgcccc                                                               >  1:275924/1‑148 (MQ=255)                                                                                          gAAAGAGTATCCGAAAACGGCGGTTAACGTGA‑TTGGTTATACCGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGCCGCATCCGTACt                                                      <  2:28973/151‑1 (MQ=255)                                                                                           aaaGAGTATCCGAAAACGGCGGTTAAAGTGC‑ATGGGTATAACGACAGCACGGGGGGGCACGACCTGAACATGCGTCTCTCCCCCCAACGGGCGGGTTTCGTTGCCAGCGCGTTGATCACCCCCGGCGTGGGCGCCAGCCGCATCCCTACTc                                                     >  2:380834/1‑151 (MQ=255)                                                                                            aaGAGTATCCGAAAACGGCGGTTAACGTGA‑TTGGTTATACCGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCACCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGCCGCATCCGTACTc                                                     <  2:526516/150‑1 (MQ=255)                                                                                                     cGAAAACGGCGGTTAACGTGA‑TTGGTTATACCGACAGCCCGGGGGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGGTTCCGTTGCCCGCGCGTTGATCACCCAGGGCGGGGACGCCAGCCGCATCCGTACTCAGGGGCTTgg                                           >  1:226342/1‑151 (MQ=255)                                                                                                                gTTAACGTGA‑TTGGTTATACCGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGCCGCATCCGTACTCAGGGCCTTGGCCCGGCTAAcc                                >  1:893643/1‑151 (MQ=255)                                                                                                                  tAACGTGA‑TTGGTTATACCGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGCCGCATCCGTACTCAGGGCCTTGGCCCGGCTAAccc                               <  1:737256/150‑1 (MQ=255)                                                                                                                   aaCGTGA‑TTGGTTATACCGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGCCGCATCCGTACTCAGGGCCTTGGCCCGGCTAACCCa                              >  1:879990/1‑150 (MQ=255)                                                                                                                     cGTGA‑TTGGTTATACCGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGCCGCATCCGTACTCAGGGCCTTGGCCCGGCTAACCCAATc                           <  2:521418/151‑1 (MQ=255)                                                                                                                       tGA‑TTGGTTATACCGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGCCGCATCCGTACTCAGGGCCTTGGCCCGGCTAACCCAATCGc                         >  1:291994/1‑151 (MQ=255)                                                                                                                           ttGGTTATACCGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGCCGCATCCGTACTCAGGGCCTTGGCCCGGCTAACCCAATCGCCa                       <  2:771677/150‑1 (MQ=255)                                                                                                                           ttGGTTATACCGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGCCGCATCCGTACTCAGGGCCTTGGCCCGCCTAACCCAATCGCCa                       <  1:246842/150‑1 (MQ=255)                                                                                                                            tGGTTATACCGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGCCGCATCCGTACTCAGGGCCTTGGCCCGGCTAACCCAATCGCCAg                      <  1:732456/150‑1 (MQ=255)                                                                                                                                     cGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGCCGCATCCGTACTCAGGGCCTTGGCCCGGCTAACCCAATCGCCAGCAACAGCAcc            <  1:836522/151‑1 (MQ=255)                                                                                                                                      gACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGCCGCATCCGTACTCAGGGCCTTGGCCCGGCTAACCCAATCGCCAGCAACAGCACCg           >  1:602096/1‑151 (MQ=255)                                                                                                                                      gACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGCCGCATCCGTACTCAGGGCCTTGGCCCGGCTAACCCAATCGCCAGCAACAGCACCg           >  2:950748/1‑151 (MQ=255)                                                                                                                                      gACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGCCGCATCCGTACTCAGGGCCTTGGCCCGGCTAACCCAATCGCCAGCAACAGCACCg           <  2:113716/151‑1 (MQ=255)                                                                                                                                        cAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGCCGCATCCGTACTCAGGGCCTTGGCCCGGCTAACCCAATCGCCAGCAACAGCACCGCa         <  2:367975/151‑1 (MQ=255)                                                                                                                                          gCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGCCGCATCCGTACTCAGGGCCTTGGCCCGGCTAACCCAATCGCCAGCAACAGCACCGCAGa       <  1:236429/151‑1 (MQ=255)                                                                                                                                          gCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGCCGCATCCGTACTCAGGGCCTTGGCCCGGCTAACCCAATCGCCAGCAACAGCACCGCAGa       <  1:951350/151‑1 (MQ=255)                                                                                                                                                gtggtCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGCCGCATCCGTACTCAGGGCCTTGGCCCGGCTAACCCAATCGCCAGCAACAGCACCGCAGAAGGTa  >  2:366325/1‑150 (MQ=255)                                                                                                                                                 |                                                                                                                                                     AATATGCCGAACAATGTGACCTTCGACAGCAGCAGCGCGACCCTGAAACCGGCGGGCGCTAACACCCTGACCGGCGTGGCAATGGTACTGAAAGAGTATCCGAAAACGGCGGTTAACGTGA‑TTGGTTATACCGACAGCACGGGTGGTCACGACCTGAACATGCGTCTCTCCCAGCAACGTGCGGATTCCGTTGCCAGCGCGTTGATCACCCAGGGCGTGGACGCCAGCCGCATCCGTACTCAGGGCCTTGGCCCGGCTAACCCAATCGCCAGCAACAGCACCGCAGAAGGTA  >  NC_000913/3716871‑3717162

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑