Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	ACB122	3,244,498	A→C	27.7%	E94A (GAG→GCG)	ureF →	Urease accessory protein UreF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	ACB122	3,244,498	0	A	C	27.7%	55.7 / 4.6	52	E94A (GAG→GCG)	ureF	Urease accessory protein UreF
Reads supporting (aligned to +/- strand):  ref base A (16/18);  new base C (11/5);  total (27/25)
Fisher's exact test for biased strand distribution p-value = 2.25e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGAGCAGGTTCACGACACATTGGCCTGCCTCGACTGGCCGGTGCTGGCGCGTCTGTACCACGCCTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAACAGCAGCGCGGCGCAGCGCTGGCGCGGTTGCTCGACGGCTGGCAACTGGGCCAGGCACCGGCCTGGCGCGCCAGCCTTGAGCTGACTCAGTTGGGCGGTATGGCCTGGCTGGCTGCAC  >  ACB122/3244364‑3244632                                                                                                                                        |                                                                                                                                       tGAGCAGGTTCACGACACATTGGCCTGCCTCGACTGGCCGGTGCTGGCGCGTCTGTACCACGCCTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGa                                                                                                                                        <  1:212249/135‑1 (MQ=255)             cGACACATTGGCCTGCCTCGACTGGCCGGTGCTGGCGCGTCTGTACCACGCCTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGGCGGGTCTTGCTGGCCAA‑CCGCGAAACCGCCGAGCTGCGCCTGgaa                                                                                                                           <  4:160425/136‑1 (MQ=255)                     tGGCCTGCCTCGACTGGCCGGTGCTGGCGCGTCTGTACCACGCCTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAAcagca                                                                                                                   >  7:332719/1‑136 (MQ=255)                      ggCCTGCCTCGACTGGCCGGTGCTGGCGCGTCTGTACCACGCCTGCCAGGCTAAAGACGCCGAAGCGGTCGGCCACTGGAGTCGGGTGGTTCTGGCCCA‑CCGCCCCACCCCCCCCCGGCGCCGGGAAGAAcacca                                                                                                                   >  1:149229/1‑135 (MQ=255)                            ccgcGACGGGCGGGGGCGGGCGCGGCTGTACCCCGCCGGCCCGGCAAAAGACGCCGAAGCGTTCGGCCACGGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAACAGCAGcgcg                                                                                                              <  7:376887/131‑1 (MQ=255)                             ctCGACTGGCCGGTGCTGGCGCGTCTGTACCACGCCTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAACAGCAGcgcg                                                                                                              <  6:156927/133‑1 (MQ=255)                               cGACTGGCCGGTGCTGGCGCGTCTGTACCACGCCTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCCCTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGCGCTGCGCCGGGAAGAACAGCCGCGCGGCGCa                                                                                                         >  4:31268/1‑136 (MQ=255)                               cGACTGGCCGGTGCTGGCGCGTCTGTACCACGCCTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGCGCTGCGCCGGGAAGAAACGCAGCGCGgcgcc                                                                                                         >  7:319041/1‑135 (MQ=255)                                gACTGGCCGGTGCTGGCGCGTCTGTACCACGCCTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGGTCTTGGTGGCCAA‑CCGCGCAACCCCCCCCCGGCGCCGGGGAGCACCGCACCGCGgcgcc                                                                                                         >  5:77329/1‑134 (MQ=255)                                        ggTGCTGGCGCGTCTGTACCACGCCTGCCAGGCTAAAGACGCCGAAGCGTTCGCCCACTGTAGGCGGGTCTTGCTGGCCAA‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAACAGCAGCGCGGCGCAGCGCTGgcg                                                                                                <  4:168769/136‑1 (MQ=255)                                         gTGCTGGCGCGTCTGTACCACGCCTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTGTTGGTGGCCAA‑CCCCGAAACCGCCGAGCTGCGCCGGGAAGAACCGCAGCGCGGCGCCGCGCTGgcg                                                                                                >  1:233271/1‑135 (MQ=255)                                         gTGCTGGCGCGTCTGTACCACGCCTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCCA‑CCCCGCAACCGCCCCCCTGCGCCGGGAAGAACAGCCGCGCGGCGCCGCCCGGgcgc                                                                                               >  8:283519/1‑136 (MQ=255)                                          tGCTGGCGCGTCTGTACCACGCCTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAACAGCAGCGCGGCGCAGCGCTGgcgc                                                                                               <  2:25974/135‑1 (MQ=255)                                                       gTACCACGCCTTCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAAGCGCAGCGCGGCGCAGCGCTGGCGCGGTTGCTCGaacgc                                                                                 >  8:64562/1‑132 (MQ=255)                                                       gTACCACGCCTGCCAGGCTAAAGCCGCCGAAGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGACACCGCCGCGCTGCGCCTGGAAGAACAGCACCGCGGCGCAGCGCTGGCGCGGTTGGTCGACGGc                                                                                 >  4:294530/1‑136 (MQ=255)                                                       gTACCACGCCTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTCTTTCTGGCCAA‑CCGCCAAACCGCCGAGCTGCGCCTGGAAGAACAGCAGCGCCGCGCAGCGCTGGCCCGGTTGCTCGACGGc                                                                                 >  4:101342/1‑136 (MQ=255)                                                       gTACCACGCCTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCCA‑CCGCGCAACCCCCCAGCAGCGCCTGGAAGAACAGCAGCGCGGCGCAGCGCGGGCGCGGTTTCGCGACgg                                                                                  >  2:141968/1‑135 (MQ=255)                                                       gTACCACGCCTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGGTCTTTCTGGCCCA‑CCGCGAAAACGCCGCGCTGCGCCTGGAAGCACAGCAGCGCGGCGCAGCGCTGGCGCGGTTTGTCGAAgg                                                                                  >  1:241099/1‑135 (MQ=255)                                                       gTACCACGCCTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGGTCTTGCTGGCCAA‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAACAGCAGCGCGGCGCAGCGCTGGCGCGGTTGCTCGACGGc                                                                                 >  3:184441/1‑136 (MQ=255)                                                         aCCACGCCTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTGTTGCTGGCCAC‑CCCCGAAACCGCCGCGCTGCGCCTGGAAGAACCGCAGCGCGGCGCAGCGCGGGCGCGGTTGCGCGCCGGcgg                                                                               >  3:262306/1‑134 (MQ=255)                                                            aCGCCTGCCAGGCTAACGACGCCGAAGCGGTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAACAGCAGCGCGGCGCAGCGCTGGCGCGGTTGCTCGACGGCTGGCa                                                                            <  4:78902/136‑1 (MQ=255)                                                                cTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGCGCTGCGCCTGGAAGAACAGCCGCGCGGCGCAGCGCTGGCGCGGTTGCTCGACGGCTGGCAACt                                                                         >  1:318855/1‑135 (MQ=255)                                                                cTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAACAGCAGCGCGGCGCCGCGCTGGCGCGGTTGCTCGACGGCGGGCAACt                                                                         >  5:98886/1‑135 (MQ=255)                                                                cTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAACAGCAGCGCGGCGCAGCGCTGGCGCGGTTGCTCGACGGCTGGCAACt                                                                         >  6:356133/1‑135 (MQ=255)                                                                cTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAACAGCAGCGCGGCGCAGCGCTGGCGCGGTTGCTCGACGGCTGGCAACt                                                                         >  5:162625/1‑135 (MQ=255)                                                                cTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAACAGCAGCGCGGCGCAGCGCTGGCGCGGTTGCTCGACGGCTGGCAACTg                                                                        >  7:268205/1‑136 (MQ=255)                                                                  gCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAACAGCAGCGCGGCGCAGCGCTGGCGCGGTTGCTCGACGGCTGGCAACTggg                                                                      >  3:362767/1‑136 (MQ=255)                                                                  gCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAACAGCAGCGCGGCGCAGCGCTGGCGCGGTTGCTCGACGGCTGGCAACTgg                                                                       >  2:337212/1‑135 (MQ=255)                                                                   ccAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCCAGCTGCGCCGGGAAGAACAGCAGCGCGGCGCAGCGCTGGCGCGGTTGCGCGACGGCTGGCAACgggg                                                                      >  5:301002/1‑135 (MQ=255)                                                                      ggCTAAAGACGCCGAAGCGTTCGGCCACTGGAGGCGGTGCTTGCTGGCCAA‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAACAGCAGCGCGGCGCAGCGCTGGCGCGGTTGCTCGACGGCTGGCAACTGGGCCAg                                                                  <  8:226008/136‑1 (MQ=255)                                                                                   gAAGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGCGCTGCGCCGGGCAGAACCGCAGCGCGGCGCAGCGCTGGCGCGGTTGCTCGACCGCGGGCAACTGGGCCCGGCACCGGCCggg                                                      >  1:60783/1‑135 (MQ=255)                                                                                    aaGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGCGCTGCGCCTGGAAGAACAGCAGCGCGGCGCCGCGCTGGCGCGGTTGCTCGACGGCGGGCAACTGGGCCAGGCACCGGCCTGgcg                                                    >  3:244743/1‑136 (MQ=255)                                                                                    aaGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAACAGCAGCGCGGCGCAGCGCTGGCGCGGTTGCTCGACGGCTGGCAACTGGGCCAGGCACCGGCCTGgcg                                                    >  7:72061/1‑136 (MQ=255)                                                                                     aGCGTGCGGCCACGGGCGGCGGTGCTTGCTGGCCAA‑CCGCGAACCCGCCGCGCGGCGCCGGTAAGAACCGCAGCGCGGGGCAGCGCTGGCGCGGTTGCGCGACGGCTGGCAACTGGGCCAGGCACCGGCCTGgcg                                                    <  2:2642/135‑1 (MQ=255)                                                                                               cccTGGCGGCGGTTCTTGCGGGCCAA‑CCGCGAACCCGCCGAGCGGCGCCTGGAAGAACAGCAGCGCGGCGCAGCGCTGGCGCGGTTGCTCGACGGCTGGCAACTGGGCCAGGCACCGGCCTGGCGCGCCAGCCtt                                          <  5:120740/133‑1 (MQ=255)                                                                                                agtGGAGGCGGTTTTGGCTGCCCAA‑CCCCTAACCCGCCGTGCGGCGCCTGTAAGACCAGCTGGGGGGCGCAGGGCTGGCGGGGTTGCTCGCCGGCTGGCAAGGGGGCCTGGCACCGGCCTGGCGCGCCAGCCTTg                                         <  2:2474/133‑1 (MQ=255)                                                                                                   ggcggcGGTGCTTGCTGGCCAA‑CCGCGACCCCGCCGAGCGGCGCCTGGAAGAACAGCCGCGCGGCGCAGCGCGGGCGCGGTTGCTCGACGGCTGGCAACTGGGCCAGGCACCGGCCGGGCGCGCCAGCCTTGAGc                                      <  6:104595/130‑1 (MQ=255)                                                                                                    gcgggggTTCTTGCGGGCCAC‑CCGCGAACCCGCCGCGGGGCGCCGGGAAGAACCGCAGCGCGGCGCAGGGCGGGCGGGGTTGCTCGACGGCTGGCAACTGGGCCAGGCACCGGCCTGGCGCGCCAGCCTTGAGCTg                                    <  7:283519/131‑1 (MQ=255)                                                                                                     aGTCGGTTCTTGCTGCCCAA‑CCGCTAAACCGCGGAGCGGCGCCTGGAAGAACAGCCGCGCGGCGCCGCGGTGGCGCGGTTGCTCGACGGCTGGCAAGTGGGCCAGGCACTGGCCTGGCGCGCCAGCCTTGAGCTg                                    <  6:126542/135‑1 (MQ=255)                                                                                                         ggTTCTGGCGGCCCAC‑CCGCTAACCCGCCGAGCTGCGCGGGCAAGAACAGCCGCGCGGCGCAGCGCGGGCGCGGTGGCTCGCCGGCGGGCAACGGGGCCAGGCACCGGCCTGGCGCGCCAGCCTTGAGCTGACTCa                               <  4:362767/136‑1 (MQ=255)                                                                                                             cTTGCTGCCCAA‑CCGCGAACCCGCCGAGCTGCGCCGGGAAGAACAGCCGCGCGGCGCAGCGCGGGCGCGGTGGCGCGACGGCTGGCAACTGGGCCAGGCACCGGCCGGGCGCGCCAGCCTTGAGCTGACTCAGtt                            <  2:109822/135‑1 (MQ=255)                                                                                                              ttGCTGGCCAA‑CCGCTAAACCGCCGAGCGGCGCCTGCAAGACCAGCTGGGCGGCGCAGCGCTGGGGGGGTTGCTCGACGGCTGGCAACTGGGCCAGGCACCGGCCTGGCGCGCCAGCCTTGAGCTGACTCAGtt                            <  6:98886/134‑1 (MQ=255)                                                                                                              ctagcggCCAACCCGCGACCCCGCGGTGCGGCGCCTGGAAGACCAGCCGCGCGGGGCAGCGCTGGCGCGGTTGCTCGACGGCGGGCCACTGGCCCAGGCACCGGCGTGGCGCGCCAGCCTTGAGCTGACTCAGtt                            <  6:314813/130‑1 (MQ=255)                                                                                                                ccgggCCAC‑CCGCCAACCCGCCGCGCGGCCCCGGCAAGACCCGCCGCGCGGCGCCGCGCTGGCGCGGTTGCGCGACGGCGGGCAACGGGGCCAGGCACCGGCCGGGCGCGCCAGCCTTGAGCTGACTCAGTTGGGc                        <  8:143761/133‑1 (MQ=255)                                                                                                                     ccAC‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAACAGCAGCGCGGCGCAGCGCTGGCGCGGTTGCTCGACGGCTGGCAACTGGGCCAGGCACCGGCCTGGCGCGCCAGCCTTGAGCTGACTCAGTTGGGCGGTAt                   <  4:357787/136‑1 (MQ=255)                                                                                                                      cAA‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAACAGCAGCGCGGCGCAGCGCTGGCGCGGTTGCTCGACGGCTGGCAACTGGGCCAGGCACCGGCCTGGCGCGCCAGCCTTGAGCTGCCTCAGTTGGGCGGTAt                   >  6:70278/1‑135 (MQ=255)                                                                                                                       aa‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAACAGCAGCGCGGCGCAGCGCTGGCGCGGTTGCTCGACGGCTGGCAACTGGGCCAGGCACCGGCCTGGCGCGCCAGCCTTGAGCTGACTCAGTTGGGCGGTATgg                 >  7:236762/1‑136 (MQ=255)                                                                                                                                acccgcggAGCGGCGCCGGTAAGACCCGCCGGGCGGCGCAGCGCTGGCGCGGTTGCGCGACGGCTGGCAACTGGGCCAGGCACCGGCCTGGCGCGCCAGCCTTGAGCTGACTCAGTTGGGCGGTATGGCctggctg         <  3:31268/134‑1 (MQ=255)                                                                                                                                aaCCGCCGCGCTGCGCGGGGATGACCAGCAGCGGGGGGGAGCGCTGGCGCGGTTGCGCTACGGCTGGCAACGGGGCCAGGCACCGGCCTGGCGCGCCAGCCTTGAGCTGACTCAGTTGGGCGGTATGGCctggctg         <  8:285999/136‑1 (MQ=255)                                                                                                                                aaCCGCCGAGCTGCGCCTGGAAGAACAGCAGCGCGGCGCAGCGCTGGCGCGGTTGCTCGACGGCTGGCAACTGGGCCAGGCACCGGCCTGGCGCGCCAGCCTTGAGCTGACTCAGTTGGGCGGTATGGCctggctg         <  4:244743/136‑1 (MQ=255)                                                                                                                                 cccgccgCGCGGCGCCGGGAAGCCCTGCTGCGCGGCGCCGCGCGGGCGCGGTTGCTCGCCGGCTGGCAACTGGGCCAGGCACCGGCCTGGCGCGCCAGCCTTGAGCAGACTCAGTTGGGCGGTATGGCctggctg         <  2:149229/134‑1 (MQ=255)                                                                                                                                 cccgccgAGCTGCGCCTGGAAGAACAGCTGCGCGGCGCCGGGAGGGGGGGGTTGCTCGACGGCTGCCAACTGGGCCAGGCACCGGCGTGGCGCGCCAGCCTTGAGCTGACTCAGTTGGGCGGTATGGCctggctg         <  2:235628/134‑1 (MQ=255)                                                                                                                                      cgAGCGGCGCCTGCAAGAACCGCCGCGCGGCGCAGCGCGGGGGCGGTTGCTCGACGGCGGGCAACTGGGCCAGGCACCGGCCGGGCGCGCCAGCCTTGAGCTGACTCAGTTGGGCGGTATGGCCTGGCTGGCTGc    <  2:126606/135‑1 (MQ=255)                                                                                                                                        aGCTGCGCCTGGAGGAACAGCAGCGCGGCGCAGCGCTGGCGCGGTTGCTCGACGGCTGGCAACTGGGCCCGGCACCGGCCAGGCGCGCCACCCATGAGCTGACTCAGTTGGGCGGTATGGCCTGGCTGGCTGcac  >  5:376771/1‑135 (MQ=255)                                                                                                                                        |                                                                                                                                       TGAGCAGGTTCACGACACATTGGCCTGCCTCGACTGGCCGGTGCTGGCGCGTCTGTACCACGCCTGCCAGGCTAAAGACGCCGAAGCGTTCGGCCACTGGAGTCGGTTCTTGCTGGCCAA‑CCGCGAAACCGCCGAGCTGCGCCTGGAAGAACAGCAGCGCGGCGCAGCGCTGGCGCGGTTGCTCGACGGCTGGCAACTGGGCCAGGCACCGGCCTGGCGCGCCAGCCTTGAGCTGACTCAGTTGGGCGGTATGGCCTGGCTGGCTGCAC  >  ACB122/3244364‑3244632

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑