Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	ACB143	1,770,577	0	A	C	35.6%	98.8 / 13.9	59	intergenic (+255/+37)	CJ019_01684/higA‑1	hypothetical protein/Antitoxin HigA‑1
Reads supporting (aligned to +/- strand):  ref base A (3/35);  new base C (20/1);  total (23/36)
Fisher's exact test for biased strand distribution p-value = 1.23e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GTCCCAGGCTTTGATGCCGTAGAGCGTGTAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAGACGCTGGACCGACCCGATGATCTCATCGCCGTGTTGCTGTTCGGCTGTGCGCAGATCGAAGGCCGTCTGCAGGTTGAGCC  >  ACB143/1770454‑1770705                                                                                                                             |                                                                                                                                  gTCCCAGGCTTTGATGCCGTAGAGCGTGTAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGgcg                                                                                                                        <  7:49749/135‑1 (MQ=255) gTCCCAGGCTTTGATGCCGTAGAGCGTGTAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGgcg                                                                                                                        <  7:157073/135‑1 (MQ=255)  tCCCAGGCTTTGATGCCGTAGAGCGTGTAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCCCCCCCGTGgcgc                                                                                                                       >  6:170749/1‑135 (MQ=255)  tCCCAGGCTTTGATGCCGTAGAGCGTGTAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGGGGCGcc                                                                                                                      >  4:295532/1‑136 (MQ=255)   cccAGGCTTTGCTGCCGTAGAGCGTGTAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCCCGCCCCGGGCGcc                                                                                                                      >  8:3884/1‑135 (MQ=255)   cccAGGCTTTGATGCCGTAGAGCGTGTAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCCCCCCCCTGGCGcc                                                                                                                      >  1:347645/1‑135 (MQ=255)   cccAGGCTTTGATGCCGTAGAGCGTGTAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGcc                                                                                                                      <  5:83749/135‑1 (MQ=255)   cccAGGCTTTGATGCCGTAGAGCGTGTAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGcc                                                                                                                      <  5:340835/135‑1 (MQ=255)         cTTTGATGCCGTAGAGCGTGTAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGtt                                                                                                                <  8:328750/135‑1 (MQ=255)              aTGCCGTAGAGCGTGTAGGTCATTGTGTACATTGGTGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGTCG‑CCACGCCCGTGGCGCCCCTGTT‑TAtt                                                                                                           <  5:384900/134‑1 (MQ=255)              aTGCCGTAGAGCGTGTAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TAtt                                                                                                           <  7:260806/134‑1 (MQ=255)              aTGCCGTAGAGCGTGTAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TAtt                                                                                                           <  7:236541/134‑1 (MQ=255)              aTGCCGTAGAGCGTGTAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TAtt                                                                                                           <  5:44211/134‑1 (MQ=255)               ttccGTAGAGCGTGTATGGCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTg                                                                                                          <  8:372948/132‑1 (MQ=255)               tGCCGTAGAGCGTGTAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTg                                                                                                          <  1:134722/134‑1 (MQ=255)               tGCCGTAGAGCGTGTAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTg                                                                                                          <  6:195767/134‑1 (MQ=255)                gCCGTAGAGCGTGTAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCC‑CACCCCCCGGGGGGCCCCGGTT‑TTTTGa                                                                                                         >  8:98703/1‑134 (MQ=255)                   gTAGAGCGTGTAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAg                                                                                                     <  6:159524/135‑1 (MQ=255)                    tAGAGCGTGTAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGGG‑CCCCCCCCCGGGGGCCCCCGTTGTATTgtgatg                                                                                                     >  6:47644/1‑130 (MQ=255)                     agagCGTGTAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGAAACGATCCTCGCGGCG‑CCCCGCCCGGGGGGCCCCGGGT‑TATTGATTAGGa                                                                                                   >  1:300379/1‑135 (MQ=255)                         cGTGTAGGTCATTGTGTACATTGGGGTTGAAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATgtgt                                                                                              <  3:80414/136‑1 (MQ=255)                            gtAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCCCCCCCCGGGCGCCCCCGGT‑GATTGTTAAAGATTTGtt                                                                                             >  2:369164/1‑134 (MQ=255)                            gtAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGGCCGATGGGACCCCGTG‑TTTTGATGAAGATTTGtt                                                                                             >  8:165183/1‑134 (MQ=255)                            gtAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCC‑CCACGCACGGGTGGCCCCAGGT‑TATTTATAAAGAttgttt                                                                                             >  8:170514/1‑129 (MQ=255)                              aGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCCCCCCCGGGGCGCCCCGGTT‑TTTTTGTCAGGTTGTGTTaaa                                                                                          >  5:157611/1‑135 (MQ=255)                              aGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCCCCCCCGGGGCGCCCCGGGT‑TTTTGTTGAGGGTTTGTTTAAg                                                                                         >  3:201645/1‑136 (MQ=255)                               ggTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCGCCCCCGCCCGGGGCCCCCCGGTT‑T‑TTGATAAGGGAGTGTTGaat                                                                                         >  8:102051/1‑134 (MQ=255)                                ggcATTGTGTACATTGGGGTGGCAAGTAGCCCCAATCTCTTCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCg                                                                                       <  4:28578/134‑1 (MQ=255)                                       tgaaCATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAg                                                                                  <  5:171026/131‑1 (MQ=255)                                        gtACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGGG‑CCCCCCCCCGGGGGGCCCGGGT‑TTTTTTTTAGGGTGTGTTGAATCCACCCGAcc                                                                               >  4:173652/1‑135 (MQ=255)                                           cATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAGACGCt                                                                             <  3:94375/135‑1 (MQ=255)                                                 ggTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCCCGCCCGGGGCGCCCCGGGT‑TATTGATGAGGATGTGTTGAAGCGCCCAGCCGCTGggccg                                                                       >  1:374906/1‑135 (MQ=255)                                                 ggTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCCCCCCCGGGGCGGCCCCGGT‑TTTTTTTGAGGTTGTGTTTAAGCGACCCGACGCgggggcc                                                                       >  5:323132/1‑131 (MQ=255)                                                    tGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCCCCCCCCGGGGGGCCCGGGT‑TTTTGTTCAGGTTGTGTTGAAGCGCCCCGACGCGGGACCGcccc                                                                   >  4:40379/1‑136 (MQ=255)                                                      cAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCCCGCCCGGGGCGCCCCGGGT‑TTTTGATCAGGATGTGTTAAAGCGCCCAGACGCGGGCCCGAccc                                                                   >  2:251886/1‑134 (MQ=255)                                                      cAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCCCGCCCGGGGCGCCCCCGGT‑TTTTGTTGAGGTTGTGTTCAAGCGCCCAGACGCTGGACCGcccc                                                                   >  8:314188/1‑134 (MQ=255)                                                      cAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCCCGCCCCGGGGGCCCCGGGT‑TTTTTATCAGGATTTGTTCAAACCACCAGAAGCTGggccgacc                                                                    >  8:210507/1‑133 (MQ=255)                                                        aGTAGCCCCAATCTCTCCGTTTTCCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCCCCCCCGGGGGGCCCCTGGT‑TTTTGTTGAGGGTGTGTTGAAGCGGCCAGGCGCTGGAGCGAGCCgctg                                                               >  3:249126/1‑136 (MQ=255)                                                         gTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGGG‑CCCCCCCCGGGGGGGCCCGGGT‑TTTTTTTGAGGGTGTGTTGAAGGGCCCCGACGCGGGGCCGcccccctga                                                              >  4:394609/1‑131 (MQ=255)                                                             ccccAATATCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAGACGCTGGACCGACCCGATGAtct                                                           <  6:112040/135‑1 (MQ=255)                                                               ccAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCCCCCCCCGGGCGCCCCGGTT‑TTTTGTTAAGGGTTTGTTGAAGCGACCAGACGCTGGGCCGACCCGCTGATCTCa                                                         >  4:97986/1‑135 (MQ=255)                                                                        ccGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAGACGCTGGACCGACCCGATGATCTCATCGCCg                                                   <  6:136339/132‑1 (MQ=255)                                                                          gTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAGACGCTGGACCGACCCGATGATCTCATCGCCgtg                                                 <  2:371003/132‑1 (MQ=255)                                                                            ttttCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAGACGCTGGACCGACCCGATGATCTCATCGCCGTGTTGCt                                            <  1:184187/135‑1 (MQ=255)                                                                                      cAGCCGCGGGATTAGGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTGCAAGCGACCAGACGCTGGACCGACCCGATGATCTCATCGCCGTGTTGCTGTTCGGCtgt                                  <  6:49649/135‑1 (MQ=255)                                                                                        gTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAGACGCTGGACCGACCCGATGATCTCATCGCCGTGTTGCTGTTCGGCtgtg                                 <  1:105122/134‑1 (MQ=255)                                                                                        gTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAGACGCTGGACCGACCCGATGATCTCATCGCCGTGTTGCTGTTCGGCTGTgc                                <  6:172841/135‑1 (MQ=255)                                                                                            cgGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCTCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAGACGCTGGACCGACCCGATGATCTCATCGCCGTGTTGCTGTTCGGCTGTGCGCa                             <  6:113413/134‑1 (MQ=255)                                                                                            cgGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAGACGCTGGACCGACCCGATGATCTCATCGCCGTGTTGCTGTTCGGCTGTGCGCa                             <  5:340723/134‑1 (MQ=255)                                                                                                  tATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAGACGCTGGACCGACCCGATGATCTCATCGCCGTGTTGCTGTTCGGCTGTGCGCAGATCGaa                      <  6:378063/135‑1 (MQ=255)                                                                                                  tATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAGACGCTGGACCGACCCGATGATCTCATCGCCGTGTTGCTGTTCGGCTGTGCGCAGATCGaa                      <  2:313098/135‑1 (MQ=255)                                                                                                    tGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAGACGCTGGACCGACCCGATGATCTCATCGCCGTGTTGCTGTTCGGCTGTGCGCAGATCGAAg                     <  2:378012/134‑1 (MQ=255)                                                                                                            cGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAGACGCTGGACCGACCCGATGATCTCATCGCCGTGTTGCTGTTCGGCTGTGCGCAGATCGAAGGCCGTCTGCa           <  4:179299/136‑1 (MQ=255)                                                                                                             gATCCTCGCGGCG‑CCCCGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAGACGCTGGACCGACCCGATGATCTCATCGCCGTGTTGCTGTTCGGCTGTGCGCAGATCGAAGGCCGTCTGCa           <  5:45316/135‑1 (MQ=255)                                                                                                                  tCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAGACGCTGGACCGACCCGATGATCTCATCGCCGTGTTGCTGTTCGGCTGTGCGCAGATCGAAGGCCGTCTGCAGGTTg      <  2:374906/135‑1 (MQ=255)                                                                                                                   cgcgGCG‑CCACGCCCGTGGCGCCCCTGTT‑TTTTGATCAGGATGTGGTCAAGCGACCAGACGCTGGACCGACCCGATGATCTCATCGCCGTGTTGCTGTTCGGCTGTGCGCAGATCGAAGGCCGTCTGCAGGTTGAg    <  3:75100/136‑1 (MQ=255)                                                                                                                    gcggcg‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAGACGCTGGACCGACCCGATGATCTCATCGCCGTGTTGCTGTTCGGCTGTGCGCAGATCGAAGGCCGTCTGCAGGTTGAg    <  3:379660/135‑1 (MQ=255)                                                                                                                     cggcg‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAGACGCTGGACCGACCCGATGATCTCATCGCCGTGTTGCTGTTCGGCTGTGCGCAGATCGAAGGCCGTCTGCAGGTTGAg    <  7:43601/134‑1 (MQ=255)                                                                                                                      ggcg‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAGACGCTGGACCGACCCGATGATCTCATCGCCGTGTTGCTGTTCGGCTGTGCGCAGATCGAAGGCCGTCTGCAGGTTGAGcc  <  7:72462/135‑1 (MQ=255)                                                                                                                             |                                                                                                                                  GTCCCAGGCTTTGATGCCGTAGAGCGTGTAGGTCATTGTGTACATTGGGGTTGCAAGTAGCCCCAATCTCTCCGTTTTTCGATGTCAGTCGCGGGATTATGCGGGAACGATCCTCGCGGCG‑CCACGCCCGTGGCGCCCCTGTT‑TATTGATCAGGATGTGTTCAAGCGACCAGACGCTGGACCGACCCGATGATCTCATCGCCGTGTTGCTGTTCGGCTGTGCGCAGATCGAAGGCCGTCTGCAGGTTGAGCC  >  ACB143/1770454‑1770705

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑