Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,486,580	0	A	G	43.8%	60.6 / 16.3	48	G121G (GGA→GGG)	lptF	lipopolysaccharide export ABC permease
Reads supporting (aligned to +/- strand):  ref base A (3/24);  new base G (21/0);  total (24/24)
Fisher's exact test for biased strand distribution p-value = 1.81e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGATGACGCTGGGCAAACTGTATACCGAAAGTGAAATTACGGTAATGCATGCCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAACCCTGGCATGGCGGC‑GCTGGCGCAAGGGCAATTCCAGCAAGCGACTAATGGCAGCTCGGTGCTGTTCATCGAAAGCGTTGACGGCAGCGATTTCA  >  NC_000913/4486434‑4486725                                                                                                                                                   |                                                                                                                                                   ctgATGACGCTGGGCAAACTGTATACCGAAAGTGAAATTACGGTAATGCATGCCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGCTAACATGCTGTGGGGGGGGCCg                                                                                                                                                 >  2:439174/1‑150 (MQ=255)      gaCGCTGGGCAAACTGTATACCGAAAGTGAAATTACGGTAATGCATGCCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGATGTGGGCGGGACCGTGGTCa                                                                                                                                           <  1:688485/151‑1 (MQ=255)        cGCTGGGCAAACTGTATACCGAAAGTGAAATTACGGTAATGCATGCCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAAAGTGAGGTGGGCGGGACCgggg                                                                                                                                              >  2:713912/1‑146 (MQ=255)            gggCAAACTGTATACCGAAAGTGAAATTACGGTAATGCATGCCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGATGTGGGCGGGACCGTGGTCATcgcg                                                                                                                                      <  1:740230/150‑1 (MQ=255)            gggCAAACTGTATACCGAAAGTGAAATTACGGTAATGCATGCCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGGGATGGGGGGGGGGcccggg                                                                                                                                              >  1:700416/1‑138 (MQ=255)               cAAACTGTATACCGAAAGTGAAATTACGGTAATGCATGCCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTTAAGTGATGTGGGGGGGGCCGCGGGCATTGCGtca                                                                                                                                   >  1:79361/1‑150 (MQ=255)               cAAACTGTATACCGAAAGTGAAATTACGGTAATGCATGCCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGATGTGGGCGGGACCGTGGTCATCGCGtcat                                                                                                                                  <  2:160559/151‑1 (MQ=255)                aaaCTGTATACCGAAAGTGAAATTACGGTAATGCATGCCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGATGTGGGGGGGGGCGGGGGCATagcg                                                                                                                                      >  1:163173/1‑146 (MQ=255)                           cGAAAGTGAAATTACGGTAATGCATGCCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAAAATGCTGTGGGCGGGGGCGGGGGGCTCGCGTCATCAGGGGGAAggg                                                                                                                      >  2:520362/1‑149 (MQ=255)                            gAAAGTGAAATTACGGTAATGCATGCCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTTAAGGGGTTTGGGCGGGGCCGTGGGGCTCGCGTGCTCCGGAGGaaagg                                                                                                                      >  1:92877/1‑147 (MQ=255)                                       tACGGTAATGCATGCCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTTACGTGATGTGGGGGGGGCCGGGGGCCTCGCGGCATCAGGGTGAAGGGGTAGCAGaa                                                                                                             >  1:513456/1‑148 (MQ=255)                                            tAATGCATGCCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGATTGGGGGGGGGCCGTGGGCCTCGCGTCCTCAGGGTGGAGGGGTAGGAGaagcggaa                                                                                                       >  2:808288/1‑149 (MQ=255)                                             aaTGCATGCCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGaagcgaaagc                                                                                                     <  1:284601/150‑1 (MQ=255)                                             aaTGCATGCCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAAAGTGATGTGGGCGGGGCCGGGGGCATCGCGTCATCAGGATGGAGGGTTTGCAGaagcgaa                                                                                                        >  1:505516/1‑147 (MQ=255)                                              atgcatgcCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGGTGTGGGCGGGGCCGGGGGCCTCGCGTCATCAGGGAGAAGGGTTTGGAGaaacgaaa                                                                                                       >  1:493666/1‑147 (MQ=255)                                                gcatgcCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTTACGGGGTGTGGGGGGGGCCGGGGGGCTCGCGGCCTCCGGAGGGAGGGGTAAGAGaagcgaaa                                                                                                       >  2:119322/1‑145 (MQ=255)                                                gcatgcCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAagcgaaagcgaa                                                                                                  <  2:261692/150‑1 (MQ=255)                                                gcatgcCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAAc                                                                                                 <  2:489826/151‑1 (MQ=255)                                                 catgcCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAAcc                                                                                                <  2:222540/151‑1 (MQ=255)                                                  atgcCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTTAAGGGGTGTGGGGGGGGCCGGGGGCATCGCGGCATCAGGATGGAGGGTTAGCAGAAGCGAAAACGAAacc                                                                                               >  1:420663/1‑151 (MQ=255)                                                  atgcCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGGTAACGTGATGTGGGGGGGGCCGCGGGGATCGCGGGATCAGGGTGAAGGGTTAGGAGaaacgaaaaggaaacc                                                                                               >  1:162932/1‑143 (MQ=255)                                                    gcCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAAAGGGGTTTTGGGGGGGGCGCGGGGCTCGCGTCATCAGGGGGGAGGGTTAGCAGgagcggaagagacaccc                                                                                              >  2:247172/1‑145 (MQ=255)                                                          ggCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAAGCCTGGCATgg                                                                                       <  2:213800/151‑1 (MQ=255)                                                           gCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAACCCTGGCATggc                                                                                      <  2:21045/151‑1 (MQ=255)                                                              tGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTTAAGTGGTGTGGGGGGGGCCGGGGGCATCGCGGCCTCAGGGTGGAGGGTTAGCAGAAGGGAAAACGAAACCCCGCAAggcgg                                                                                    >  1:263406/1‑150 (MQ=255)                                                                  cAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAACCCTGTCATGGCGGC‑GCt                                                                               <  2:322269/150‑1 (MQ=255)                                                                  cAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAAAGTGGTGTGGGGGGGGGCGGGGGCATCGCGTCATCCTGGTGAAGTGTTTGTAGAAACGGAAACGGAACCtcggaaggggggg                                                                                  >  2:443644/1‑136 (MQ=255)                                                                   aaaGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAACCCTGGCATGGCGGC‑GCTgg                                                                             <  2:471635/151‑1 (MQ=255)                                                                      gCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTTACCGGATTTGGGCGGGGCCGGGGTCATCGCCTCCTCCAGGTGAAATGTTTGGAGAAGCGAAAGCGAACCCCGGCATAGGGGC‑GCTgg                                                                             >  1:179708/1‑148 (MQ=255)                                                                      gCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAAAGTGATGTGGGGGGGGCCCGGGGCATCGCGTCCTCAGGGTGAAGGGGTAGCAGAAGCGGAAAGGAACCCCGGCATggggggggcgggg                                                                            >  2:55226/1‑142 (MQ=255)                                                                              ggTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAACCCTGGCATGGCGGC‑GCTGGCGCAAGGGCa                                                                   <  2:816122/150‑1 (MQ=255)                                                                                    aGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTGTACATGGTATTGGGGGGAACCTGGGCGTCGCGCCATCTCGATGAAGGGGTAGAACAAGCGTAACCGGACCCTGGCCTGGCGGC‑GCGGgcggcgggggaact                                                                >  1:415925/1‑136 (MQ=255)                                                                                         cAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGATGTGGGCCGGGCCGGGGGCATCGCGCCCTCAGGGTGAAAAGGTAGAAGAAGCGAAAAAGAAACCCGGCACGGCGGC‑GCTGGGGCCAGGGCAATTTcaacaaa                                                        >  1:641280/1‑149 (MQ=255)                                                                                             gATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAACCCTGGCATGGCGGC‑GCTGGCGCAAGGGCAATTCCAGCAAGCGACt                                                   <  1:646988/151‑1 (MQ=255)                                                                                                ccTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAACCCTGGCATGGCGGC‑GCTGGCGCAAGGGCAATTCCAGCAAGCGACTAAt                                                <  2:163143/151‑1 (MQ=255)                                                                                                 cTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGATGTGGGCGGGGCCGTGGGCATCGCGGCATCAGGATGAAGTGTTAGCAGAAGCGGAAGCGAACCCCGGCATGGCGGG‑GCCGGCGCAAGGGCAAATCCCGCa                                                          >  2:687182/1‑140 (MQ=255)                                                                                                       gTATTCACGGCAATCGTAGCGGCGGTTAAAGTGATGTGGGGGGGGCCGGGGGGCTCGCGGCATCCGGGGGGAGGGGTAGCAGAAGGGAAAACGAACCCCGGCATGGCGGCGGCGGGGGCAGGGGAAATT‑CAGCAAACGGCTaaatg                                              >  1:82014/1‑143 (MQ=255)                                                                                                           tCACGGCAATCGTAGCGGCGGTTAACGTGATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAACCCTGGCATGGCGGC‑GCTGGCGCAAGGGCAATTCCAGCAAGCGACTAATGGCAGCTCgg                                      <  1:161752/150‑1 (MQ=255)                                                                                                              cGGCAATCGTAGCGGCGGTTAACGTGATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAACCCTGGCATGGCGGC‑GCTGGCGCAAGGGCAATTCCAGCAAGCGACTAATGGCAGCTCGGTGCt                                  <  1:487135/151‑1 (MQ=255)                                                                                                                     cGTAGCGGCGGTTAACGTGATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAACCCTGGCATGGCGGC‑GCTGGCGCAAGGGCAATTCCAGCAAGCGACTAATGGCAGCTCGGTGCTGTTCATc                           <  1:658823/151‑1 (MQ=255)                                                                                                                      gTAGCGGCGGTTAACGTGATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAACCCTGGCATGGCGGC‑GCTGGCGCAAGGGCAATTCCAGCAAGCGACTAATGGCAGCTCGGTGCTGTTCATCg                          <  2:453107/151‑1 (MQ=255)                                                                                                                                  aaCGTGATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAACCCTGGCATGGCGGC‑GCTGGCGCAAGGGCAATTCCAGCAAGCGACTAATGGCAGCTCGGTGCTGTTCATCGAAAGCGTTGACg              <  1:55236/151‑1 (MQ=255)                                                                                                                                  aaCGTGATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAACCCTGGCATGGCGGC‑GCTGGCGCAAGGGCAATTCCAGCAAGCGACTAATGGCAGCTCGGTGCTGTTCATCGAAAGCGTTGACg              <  1:775063/151‑1 (MQ=255)                                                                                                                                    cGTGATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAACCCTGGCATGGCGGC‑GCTGGCGCAAGGGCAATTCCAGCAAGCGACTAATGGCAGCTCGGTGCTGTTCATCGAAAGCGTTGACGGc            <  2:807329/151‑1 (MQ=255)                                                                                                                                       gATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAACCCTGGCATGGCGGC‑GCTGGCGCAAGGGCAATTCCAGCAAGCGACTAATGGCAGCTCGGTGCTGTTCATCGAAAGCGTTGACGGCAg          <  2:69214/150‑1 (MQ=255)                                                                                                                                         tgtgGGCGGGACCGTGGTCATCGAGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAACCCTAGCATGGCGGC‑GCTGGATCAAGGACAATTCCAGCAAGCGACGAATGGCAGGTCCGTGCTGTTCATCTAAAGCGTTGACGGCAGCg        <  2:539144/150‑1 (MQ=255)                                                                                                                                            gggCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAACCCTGGCATGGCGGC‑GCTGGCGCAAGGGCAATTCCAGCAAGCGACTAATGGCAGCTCGGTGCTGTTCATCGAAAGCGTTGACGGCAGCGAttt    <  2:544991/151‑1 (MQ=255)                                                                                                                                               cGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAACCCTGGCATGGCGGC‑GCTGGCGCAAGGGCAATTCCAGCAAGCGACTAATGGCAGCTCGGTGCTGTTCATCGAAAGCGTTGACGGCAGCGATTTCa  >  1:78649/1‑150 (MQ=255)                                                                                                                                                   |                                                                                                                                                   CTGATGACGCTGGGCAAACTGTATACCGAAAGTGAAATTACGGTAATGCATGCCTGCGGCCTGAGCAAAGCGGTTCTGGTGAAAGCGGCAATGATCCTTGCGGTATTCACGGCAATCGTAGCGGCGGTTAACGTGATGTGGGCGGGACCGTGGTCATCGCGTCATCAGGATGAAGTGTTAGCAGAAGCGAAAGCGAACCCTGGCATGGCGGC‑GCTGGCGCAAGGGCAATTCCAGCAAGCGACTAATGGCAGCTCGGTGCTGTTCATCGAAAGCGTTGACGGCAGCGATTTCA  >  NC_000913/4486434‑4486725

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑