Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,999,3710CT50.0% 24.1 / 20.7 32intergenic (‑226/‑253)ygeV/ygeWsigma‑54‑dependent Fis family transcriptional regulator/knotted carbamoyltransferase YgeW
Reads supporting (aligned to +/- strand):  ref base C (7/9);  new base T (16/0);  total (23/9)
Fisher's exact test for biased strand distribution p-value = 8.16e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

AGAGATATCACATTTCTATATCAATATGAGAATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATT  >  NZ_CP009273/2999283‑2999455
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agagATATCACATTTCTATATCAATATGAGAATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCt                                                                                     <  2:908482/90‑1 (MQ=255)
   gaTATCACATTTCTATATCAATATGAGAATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGAt                                                                                  <  1:1038807/90‑1 (MQ=255)
     tatCACATTTCTATATCAATATGAGAATTACGGCGGTGAGTTTTTCAAAATGAAGAGAGATAGCCTGCCCCCTTATCTTTTTTTTTATAc                                                                                >  2:617299/1‑90 (MQ=255)
     tatCACATTTCTATATCAATATGAGAATTACGGCGGTGAGGTTATCAAAATGAAGAGAGATAGCCTGCCCCTTTTTCTTATTTTTGATAc                                                                                >  2:530856/1‑90 (MQ=255)
           aTTTCTATATCAATATGAGAATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTagca                                                                          <  1:32420/90‑1 (MQ=255)
            tttCTATATCAATATGAGAATTACGGCGGTGGGGTTTTCAAAATGAAGAGAGAAAGCCTGCCCCCTTTTCTTTTTTTTTATACTTaacag                                                                         >  2:1165632/1‑90 (MQ=255)
            tttCTATATCAATATGAGAATTACGGCGGTGAGGTTTTCAAACTGAAGAGAGATAACCTGCCCCTTTATCTTTTTTTTGATACTTagcag                                                                         >  1:287779/1‑90 (MQ=255)
                 atatCAATATGAGAATTACGGCGGGGAGGTTTTTAAAACCAAAAGAGAAAAACTGCCCCTTTTTTTTTTTTTTTATTATTTGAAGCaaaa                                                                    >  1:753159/1‑89 (MQ=255)
                    tCAATATGAGAATTACGGCGGTGAGGTTTTTAAAATTAAGAGAGATAGCCTGCCCCCTTTTTTTTTTTTTTATAATTAACAGCaaaaaaa                                                                 >  1:233065/1‑90 (MQ=255)
                     cAATATGAGAATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCaaataaat                                                                <  2:287779/90‑1 (MQ=255)
                      aaTATGAGAATTACGGCGGTGTGTTTTTTAAAATGAAAAGAGGGAGGCTGCCCCTTTTTTTTATTTTTTATAATTAAAAGGaaaaaaaaa                                                               >  2:1241888/1‑88 (MQ=255)
                      aaTATGAGAATTACGGCGGTGGGGTTTTTAAAATTAAAAAAGAAAAACTTCCCCCTTTTTTTTTTTTTGATAATTAGCAGCAaaaaaata                                                               >  1:863597/1‑90 (MQ=255)
                      aaTATGAGAATTACGGCGGTGGGGTTTTTAAAATGAAGAGAGAAAACCTTCCCCCTTTTTTTTTTTTTTATACTTATCAGCaaataaaaa                                                               >  1:308012/1‑88 (MQ=255)
                      aaTATGAGAATTACGGCGGTGAGTTTTTTAAAATGAAGAGAGATAGCCTGCCCCCTTTTCTTTTTTTTTATAATTTACAGCaaaaaaaaa                                                               >  2:932354/1‑88 (MQ=255)
                           gagaATTACGGCGGTGTGATTTTCAAACTGCAGAGAGAAAGAATGGCCCATTTTCTTTTTTTTTTTACTTTGTATCAAAAAAAAAAagcg                                                          >  1:669798/1‑90 (MQ=255)
                             gaATTACGGCGGTGAGGTTTTTAAAATGAAGAGAGAAAACCTGCCCCTTTTTCTTTTTTTTTATAATTAGCAGCAAAAAAAAAAAGCGAt                                                        >  1:782075/1‑90 (MQ=255)
                                 tACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTTTGATACTTAGCAGCAAAAAAAAAACGCGATaaaa                                                    >  2:1052145/1‑90 (MQ=255)
                                 tACGGCGGTGAGGTTTTCAAACTGAAGAGAGATAGCCTGCCCCTTTATTTTTTTTTTTATACTTAGCAGCAAAAAAATAACGCGATaaaa                                                    >  2:1052372/1‑90 (MQ=255)
                                       ggTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTTTCTTTTTTTTGATACTTAGCAGCAAAAAAATAAAGCGATAAAAAAAAcc                                              >  1:131042/1‑90 (MQ=255)
                                       ggTGAGGTTTTTAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTTTTATACTTAGCAGCAAAAAAAAAAAGCGATaaaaaaaaac                                              >  1:115114/1‑87 (MQ=255)
                                                            agagaTAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTacaa                         <  1:1052145/90‑1 (MQ=255)
                                                            agagaTAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTacaa                         <  1:372133/90‑1 (MQ=255)
                                                              agaTAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTacaaac                       <  2:377409/90‑1 (MQ=255)
                                                                  aGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAAcc                   >  2:116970/1‑90 (MQ=255)
                                                                  aGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAAcc                   >  1:948512/1‑90 (MQ=255)
                                                                       gCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGaac              >  1:1203315/1‑89 (MQ=255)
                                                                       gCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAg              >  1:931190/1‑90 (MQ=255)
                                                                       gCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAg              >  1:707107/1‑90 (MQ=255)
                                                                         cccTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCt            <  2:481733/90‑1 (MQ=255)
                                                                            tttATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGc         >  2:529749/1‑90 (MQ=255)
                                                                                 cTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCaa    >  1:977159/1‑90 (MQ=255)
                                                                                   tATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAAtt  <  1:628824/90‑1 (MQ=255)
                                                                                        |                                                                                    
AGAGATATCACATTTCTATATCAATATGAGAATTACGGCGGTGAGTTTATCAAACTGAAGAGAGATAGCCTGCCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATT  >  NZ_CP009273/2999283‑2999455

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑