Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	5,384,266	0	T	G	30.2%	87.0 / 11.0	53	intergenic (+529/‑329)	CJ019_05064/CJ019_05067	putative protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (5/32);  new base G (16/0);  total (21/32)
Fisher's exact test for biased strand distribution p-value = 1.37e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GCCCGTCGGGCGGCTGCGGATTAAATCAGTAGACACGGCTAAGCATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTAGGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCATTTTTTCAGGGTTTTAGTCTCGGTG  >  KT2440/5384133‑5384400                                                                                                                                      |                                                                                                                                       gCCCGTCGGGCGGCTGCGGATTAAATCAGTAGACACGGCTAAGCATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTGtttt                                                                                                                                     >  1:294616/1‑137 (MQ=255) gCCCGTCGGGCGGCTGCGGATTAAATCAGTAGACACGGCTAAGCATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCtgtt                                                                                                                                     >  1:389787/1‑137 (MQ=255)      tCGGGCGGCTGCGGATTAAATCAGTAGACACGGCTAAGCATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTtgt                                                                                                                                <  4:436596/137‑1 (MQ=255)      gcGGGCGGCTGCGGATTAAATCAGTAGACACGGCTAAGCATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTtgt                                                                                                                                <  1:152002/136‑1 (MQ=255)       ggggCGGCTGCGGATTAAATCACTAGACACGGCTAAGCATGTAGAACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTtgtg                                                                                                                               <  8:498590/136‑1 (MQ=255)                                    cGGCTAAGCATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGaata                                                                                                  <  2:294616/137‑3 (MQ=255)                                        tAAGCATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTGGTTTTTTTTGTGTGGCATTTTGGGGCGGCCGGGCGCAAAAtaa                                                                                              >  8:19084/1‑135 (MQ=255)                                         aaGCATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTGGTTTTTTGTGGCGGGTATTTGGGCGCTGCGGGTGGAAAAATCgg                                                                                             >  6:143330/1‑137 (MQ=255)                                            cATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAATGAAGAAGACGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGAtt                                                                                          <  5:200149/137‑1 (MQ=255)                                            cATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGAtt                                                                                          <  8:350440/137‑1 (MQ=255)                                            cATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGAtt                                                                                          <  7:124712/137‑1 (MQ=255)                                               ttagtaCCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTaa                                                                                       <  1:362198/136‑1 (MQ=255)                                               gtagtaCCGACAGCGGAGTACTGGCGGACGTGGGTGCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTTGCGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTaa                                                                                       <  2:120606/137‑1 (MQ=255)                                               gtagtaCCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCTGGCGTCTTTTTTTGCGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTaa                                                                                       <  2:127200/137‑1 (MQ=255)                                               gtagtaCCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTaa                                                                                       <  1:155824/137‑1 (MQ=255)                                                 agtaCCGAGAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAAcc                                                                                     <  4:312794/137‑1 (MQ=255)                                                    aCCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTGGGTTTTTTTTGCTGGATTTTTGGGGCGGGGGGGGGAAAAATAGGATTTaaaacca                                                                                  >  1:310339/1‑132 (MQ=255)                                                    aCCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCGGTTTTTTTGGCTGGGATTTTGGGGGTGCGGGGCGGAAAATCGGTTTTAAcacca                                                                                  >  2:362198/1‑136 (MQ=255)                                                        aCAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTGGTTTTTTTTTGCTCGAATTTGGTGGCTGGGGGGCGAAAAATCCGATTTAAACCCattat                                                                              >  5:484520/1‑135 (MQ=255)                                                        aCAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCGTTTTTTGTGGCGGGTATTTGGGGGCGGGGGGTCGAAAAATGGGATTTAACCCCGTTcg                                                                              >  8:414744/1‑136 (MQ=255)                                                        aCAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTAGGGCGTCGTTTTTTGTGCCAGGGATTTGTGCGCTGCGGGTAGAAAAATCCGATTTACCCCCtttgt                                                                              >  6:466179/1‑135 (MQ=255)                                                         cAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTGTTTTTTTTTGGCTGGAATTTTTGGGCTGCGGGTGGAAAAAAAGGATTTAACCCCATTCtt                                                                             >  6:424053/1‑137 (MQ=255)                                                         cAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTGGTGTTTTTTTGCTGGGATTTTGGCGATGGGGGGGGAAAAAAAGGTTTTAAACCCattatt                                                                             >  7:91817/1‑137 (MQ=255)                                                           gCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTGTGTTTTTGTGGCAGGAATATGGGCGCGGGGGGGCGCAAAAACGGTGTTTAACCCTTTCTTGt                                                                           >  2:40540/1‑137 (MQ=255)                                                           gCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTGGTTTTTTGTGGCTGGAATTTTGGGGGTGCGGGTGGAAAAATCGGATTTAAACCCattatttt                                                                           >  6:198220/1‑135 (MQ=255)                                                           gCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTTTTTGCGGGAATTTGGGCGCTGCGGGGCGAAAAAAAGGATTTAACCCCGTTCTTGt                                                                           >  8:108992/1‑137 (MQ=255)                                                              gAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTTTTTCGTGGAATTTGGGGGGGGCGGGTCGAAAAATAGGATTTTACACCGTTTGTGTAgg                                                                        >  2:69845/1‑137 (MQ=255)                                                               tgTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTAggg                                                                       <  3:284513/136‑1 (MQ=255)                                                               aGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTAggg                                                                       <  2:389787/137‑1 (MQ=255)                                                                     ggCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTAGGGCGTTTc                                                                 <  3:90039/137‑1 (MQ=255)                                                                     ggCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTAGGGCGTTTc                                                                 <  1:495074/137‑1 (MQ=255)                                                                         gACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTGGTTTTTTTTGGCTGGTATTTTGGGGGGGGGGGGGGGAAAATCGGGTTTTACACCGGTATTGTAGGGCGgttggcca                                                             >  4:461013/1‑132 (MQ=255)                                                                              gggTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTGGTTTTTTTTGGCTGGTATTTTGGCGGTGCGGGGGGAAAAATAGGATTTTA‑ACCATTGTTGTAGGGCGGTTGCCAAAGATaa                                                       >  6:423972/1‑136 (MQ=255)                                                                              gggTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTGGTTTTTTTTGGCGGGTTTTTTGGGGCGGGGGGGGGTAAAATAGGCTTTTAACCCGTTGTTGTTTGGCGGTTGCCCAAGAtt                                                        >  4:460683/1‑136 (MQ=255)                                                                              gggTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTGGTTTTTTGTGGCTGGGATTTGGGGGGGGCGGGGGGAAAAATCGGCTTTAACCCCGTTCTTGTTGGGGGGTTGCCAAAGATa                                                        >  7:90337/1‑137 (MQ=255)                                                                              gggTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTGGGTTTTTGTGGCGGGGATTTGGGGGGGGCGGGGGGGAAAAAAGGATTTAACCCCGTTCTAGTTGGGCGGTTGGCAAAgctt                                                        >  7:272857/1‑134 (MQ=255)                                                                              gggTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCGTTTTTTTTTCGTGGATTTTTGGGGCTGCGGGGGGAAAAAAGGGATTTAGACCCTTTGTTTTATGGGGGTTGGCAAAgtat                                                        >  4:288113/1‑134 (MQ=255)                                                                              gggTTCAAATAACCCCGGATCCACCAAATCCAACGAAGAAGACGACCTAGTGCGTCTTTTTTTGTTCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTAGGGCGTTTCCCAAAGATa                                                        <  6:265261/137‑1 (MQ=255)                                                                                gTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTAGGGCGTTTCCCAAAGATAct                                                      <  8:498619/137‑1 (MQ=255)                                                                                gTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTAGGGCGTTTCCCAAAGATAct                                                      <  5:369993/137‑1 (MQ=255)                                                                                          ccccGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTAGGGCGTTTCCCAAAGATACTGCCTGCGCCt                                            <  7:281788/137‑1 (MQ=255)                                                                                                    accaAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTAGGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGtt                                  <  3:82527/137‑1 (MQ=255)                                                                                                                gaagaagaCGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTAGGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCAttttt                      <  5:499594/137‑1 (MQ=255)                                                                                                                gaagaagaCGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTAGGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCAttttt                      <  5:143330/137‑1 (MQ=255)                                                                                                                gaagaagaCGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTAGGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCAttttt                      <  8:318659/137‑1 (MQ=255)                                                                                                                gaagaagaCGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTAGGGCGGTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCAttttt                      <  7:448510/137‑1 (MQ=255)                                                                                                                  agaagaCGCCCTCGGGCGTGGTTTTTTTTTGGTGGGATTTTTGGGGGGGGGGGGGAAAAATAGGATTTTAACCCGTTGGTGTTGGGGGGTTGCCCAAAATAATGCCTGCGCCGGTTTTTCGTTGGGGTGTttttttt                    >  6:315647/1‑136 (MQ=255)                                                                                                                  agaagaCGCCCTCGGGCGTCTTTTTTTGTGGCTGGGATTTGGGGGCTGCGGGGGGTAAAATCGGATTTATCACCTTTCTTGTTGGGCGTTTAGCAGACATACTGCCATCGCCGGTTTTGCGTTTCGGGCAttttttt                    >  8:392571/1‑136 (MQ=255)                                                                                                                     agaCGCCCTCTGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTAGGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCATTTTTTCAgg                 <  6:423759/137‑1 (MQ=255)                                                                                                                     agaCGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTAGGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCATTTTTTCAgg                 <  4:459358/137‑1 (MQ=255)                                                                                                                          cccTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTAGGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCATTTTTTCAGGGtttt            <  7:108992/137‑1 (MQ=255)                                                                                                                               gggCGTCTTTTTTTGTGGCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACAACTTTCTTGTAGGGCGTTTCGCAATGATACTGCCTGCGCGTGTTTTCCGTTGCGGTCATTTTTTCAGGTTTTTAGtct       <  2:428666/137‑1 (MQ=255)                                                                                                                               gggCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTAGGGCGGTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCATTTTTTCAGGGTTTTAGtct       <  1:80098/137‑1 (MQ=255)                                                                                                                                ggCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTAGGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCATTTTTTCAGGGTTTTAGtctc      <  5:424053/137‑1 (MQ=255)                                                                                                                                    tCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGGCGAAAAATCGGATTTAACCCCTTTCTTGTAGGGCGTTTCCCAAAGATACTGCCTGCGGCTGTTTTCCGTTGCGGTCATTTTTTAAGTGTTTTAGTCTCGGTg  <  5:396236/137‑1 (MQ=255)                                                                                                                                      |                                                                                                                                       GCCCGTCGGGCGGCTGCGGATTAAATCAGTAGACACGGCTAAGCATGTAGTACCGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCAAATCCAAAGAAGAAGACGCCCTCGGGCGTCTTTTTTTGTGCCTGGAATTTGGGCGCTGCGGGTCGAAAAATCGGATTTAACCCCTTTCTTGTAGGGCGTTTCCCAAAGATACTGCCTGCGCCTGTTTTCCGTTGCGGTCATTTTTTCAGGGTTTTAGTCTCGGTG  >  KT2440/5384133‑5384400

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: ‑