Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092735,1590GA48.3% 23.5 / 15.2 29intergenic (+139/‑75)thrC/yaaXthreonine synthase/DUF2502 domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base G (15/0);  new base A (0/14);  total (15/14)
Fisher's exact test for biased strand distribution p-value = 1.29e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGG  >  NZ_CP009273/5027‑5291
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ttCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATaa                                                                                                                                 >  1:503844/1‑138 (MQ=255)
     tATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAAccg                                                                                                                           >  1:497426/1‑139 (MQ=255)
           aaTCAGGCCGGGTTTGCTTTTATCAAGCCCGGTTTTTTTATAAAGAAATGAGGGAGAAAAAGGACAGGGAAAAAGGAAAAATTCTCAAAAACTGGGGTAAGGAAGAAATAAGGATGGCGGAAAAAAACAAccgccg                                                                                                                        <  2:174211/136‑1 (MQ=255)
            aTCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTtct                                                                                                                    >  1:674784/1‑139 (MQ=255)
             tCAGGCCGGTTTTGTTTTTATGCACCCCGGTTTTTTTATAAAAAAATAAGGGAAAAAAATGACAGGAAAAAAGGAGAAATTCCAAATAAATGCGGTAACTAAGAGATTGGGTTGGCGGAAAATAACAACCGCCGTtctc                                                                                                                   <  2:225705/139‑1 (MQ=255)
                 gCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATc                                                                                                                >  2:151492/1‑138 (MQ=255)
                 gCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCg                                                                                                               >  2:117981/1‑139 (MQ=255)
                   ggggTTTGTTTTTATGCAGCCCGGTTTTTTTATAAAAAAATTATGAAAAAAAAGGACGGGAAAAAAGGAAAAATTCTAAAAAAAGGCGGTAACTAAGAGATTAGGATTGCGGAAAATAACAACCGCCGTTCTCATCGAg                                                                                                             <  1:538120/138‑1 (MQ=255)
                     ggTTTGCTTTTATGCAGCCCGGC‑TTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTaa                                                                                                          >  1:504780/1‑139 (MQ=255)
                      gtttgtttTTATGCAGCCCGTTTTTTTTAAAAAAAAATTATGGAAAAAAAGGACAGGAAAAAAGGAAAAATTCTCAAAAAATGCGGAAACTTAAAGATTAGGATTGCGAAAAAAAAAAACCGCCGTTCTCATCGAGTaa                                                                                                          <  2:674784/139‑1 (MQ=255)
                                 tGCAGCCCGGTTTTTTTATGAAAAAATTAGGGAAAAAAATGACAGGAAAAAAGGAAAAATTCAAAATAAATGCGGTAATTTAGAGATTAGAATTGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGatat                                                                                               <  1:598251/139‑1 (MQ=255)
                                 ggcggCCGGGTTTTTTTATAAAAAAATTAGGAAAAAAAATGACAGGAAAAAAGGAAAAATCCACAAAAAATGCGGTAACTAAGAGATAAGGATGGGGAAAAAAAAAACCCGCCGTTCTCATCGAGTAATCTCCGGatat                                                                                               <  2:107978/135‑1 (MQ=255)
                                  gCAGCCCTGTTTTTTAATGAAGAAATTAGGGAAAAAAATAACAGGAAAAAAGGAAAAATTCTAAAAAAATGCGTTAATTGAGAATTTAGGTTTGGGGAAAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATc                                                                                              <  2:51075/139‑1 (MQ=255)
                                      cccGGCTTTTTTATGAAGCAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGAcc                                                                                          >  2:465514/1‑139 (MQ=255)
                                      cccGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGAcc                                                                                          >  2:461089/1‑139 (MQ=255)
                                      cccGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGAcc                                                                                          >  2:887879/1‑139 (MQ=255)
                                           tttttttAAGAAAAAATTAGGGAAAAAAAGGACGGAAAAAAAGGAAAAATTCCAAAAAAAGGCGGTAACTAAGAAATAAGGAGGGGGAAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATaa                                                                                     <  2:520051/138‑1 (MQ=255)
                                           cTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATaa                                                                                     >  2:598251/1‑139 (MQ=255)
                                                  ataaaaaaaTTATGGAAAAAAATGACAGGAAAAAAGGAAAAATTCTAAATAAATGCGGTAACTAAGAGATTAGGATTGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCa                                                                               <  1:871435/132‑1 (MQ=255)
                                                        aaaTTAGGAAAAAAAATGACAGGGAAAAAGGAAAAATTCAAAAAAAAGGCGTAAACTGAAAGATAAGGATTGCGGAAAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATaa                                                                        <  1:569836/139‑1 (MQ=255)
                                                                           aaggaaaaaaggaaaaaTTCAAAATAAATGCGATAACTTAGAATTTAGGATGGGGAAAAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGaaaa                                                     <  2:503844/138‑1 (MQ=255)
                                                                                aaaaaGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATg                                                >  1:755689/1‑139 (MQ=255)
                                                                                          aaTTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCg                                      >  1:541565/1‑139 (MQ=255)
                                                                                               ccAAAAAAGGCTGTAACTAAGATATTAGGATTGAGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACt                                  <  2:573202/137‑1 (MQ=255)
                                                                                                        gCGTTAACTAAGAGATTAGAGTGGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTcc                        <  1:597733/139‑1 (MQ=255)
                                                                                                                  agagATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTgg              >  2:528181/1‑139 (MQ=255)
                                                                                                                        tAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTc        >  1:406651/1‑139 (MQ=255)
                                                                                                                            aTTGCGGAAAAGAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTAGCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCa     <  2:734578/138‑1 (MQ=255)
                                                                                                                                gggggaAAAACAACCGCCCGTCTCATCGAGTAATCTCCGGGTATTGACCCAAAAAGGGGAATGGTAAAAGGGGTAACCTGTGAAAAAGATGCAATTTATCGTATTCGCACTTTTCCTGGTTTTGGGCGCGCCCACgg  >  2:147655/5‑137 (MQ=255)
                                                                                                                                cGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATgg  >  2:711250/1‑137 (MQ=255)
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TTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGG  >  NZ_CP009273/5027‑5291

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑