Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913266,1430TC22.7% 89.6 / 22.6 44L137L (CTA→CTG) yafYCP4‑6 prophage; inner membrane lipoprotein YafY
Reads supporting (aligned to +/- strand):  ref base T (14/20);  new base C (7/3);  total (21/23)
Fisher's exact test for biased strand distribution p-value = 1.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.55e-02
Rejected as consensus: Frequency below/above cutoff threshold.

GAACCCCGGGATAGCAGAGGCATTAAAGCTCGCGAGCAGTACACCCGCCAGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTT  >  NC_000913/266007‑266276
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gacccccGGGATAGCGGAGGCATTACAGCGCGCGAGACGTACACCCGCCAGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGc                                                                                                                                    <  1:354544/137‑1 (MQ=255)
 aaCCCCGGGATAGCAGAGGCATTAAAGCTCGCGAGCAGTACACCCGCCAGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCt                                                                                                                                   >  1:443251/1‑140 (MQ=255)
              cAGAGGCATTAAAGCTCGCGAGCAGTACACCCGCCAGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGttt                                                                                                                      <  1:482754/140‑1 (MQ=255)
                   gCATTAAAGCTCGCGAGCAGTACACCCGCCAGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGt                                                                                                                 <  1:487801/140‑1 (MQ=255)
                     aTTAAAGCTCGCGAGCAGTACACCCGCCAGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCa                                                                                                               <  1:658564/140‑1 (MQ=255)
                             tCGCGAGCAGTACACCCGCCAGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTa                                                                                                       >  1:72986/1‑140 (MQ=255)
                                cgAGCAGTACACCCGACAGCATTAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTc                                                                                                    <  1:254120/140‑1 (MQ=255)
                                          ccccGCCAGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTAtttt                                                                                          <  1:398193/139‑1 (MQ=255)
                                              gCCAGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCtt                                                                                      <  2:72986/140‑1 (MQ=255)
                                                cAGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTg                                                                                    >  2:396674/1‑140 (MQ=255)
                                                 aGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCTGTTTGCCCTCATGGGCCTACTACAAGTATTGTTCTTTgg                                                                                   >  2:360820/1‑140 (MQ=255)
                                                 aGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCGGTTTGTCGTCATGGGCGTACTCAAAGTATTGTTCTTTgg                                                                                   >  2:330412/1‑140 (MQ=255)
                                                 aGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTAATGGGCTTACTCAGAGTATTTTTCTTTgg                                                                                   >  1:360804/1‑140 (MQ=255)
                                                   cATAAACCGACTTAGTGAAAGTATTGTCATGCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGta                                                                                 >  2:448460/1‑140 (MQ=255)
                                                              ttAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGt                                                                      <  1:464453/140‑1 (MQ=255)
                                                               tAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTc                                                                     <  1:448460/140‑1 (MQ=255)
                                                                aGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGTCGTGCTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCa                                                                    >  2:297546/1‑140 (MQ=255)
                                                                   gAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCAcct                                                                 <  1:464708/140‑1 (MQ=255)
                                                                          ttGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTa                                                          >  2:588297/1‑140 (MQ=255)
                                                                            gTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTAtt                                                        <  1:446564/140‑1 (MQ=255)
                                                                                  cTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCa                                                                    >  1:529389/1‑122 (MQ=255)
                                                                                  cTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCa                                                                    <  2:529389/122‑1 (MQ=255)
                                                                                  cTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGtt                                                  >  1:707570/1‑140 (MQ=255)
                                                                                           tttGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTAt                                         <  2:443251/140‑1 (MQ=255)
                                                                                           tttGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTAt                                         <  1:130143/140‑1 (MQ=255)
                                                                                           tttGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTAt                                         <  2:287361/140‑1 (MQ=255)
                                                                                           tttGTCGTTGTTTTACTCCTGACTGCCAGCGTTCGAGCGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTAt                                         <  1:198320/140‑1 (MQ=25)
                                                                                                   gtttttATTCCCGGTTATCAGGGTTTGACGGTATCAGCAGCCGTCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATa                                 <  1:480782/138‑1 (MQ=11)
                                                                                                     ttttATTCCCGGTTATCAGGGTTTGACGGTATCAGCAGCCGTCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATaca                               <  1:409998/140‑1 (MQ=11)
                                                                                                      tttATTCCCGGTTATCAGGGTTTGACGGTATCAGCAGCCGTCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATacac                              >  2:450793/1‑140 (MQ=11)
                                                                                                       ttATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATAcaca                             <  1:124235/140‑1 (MQ=255)
                                                                                                         aTTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAgc                           <  2:707570/140‑1 (MQ=255)
                                                                                                             ccggttatCAGGGTTTGACGGTATCAGCAGCCGTCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCAt                       <  1:30635/133‑1 (MQ=14)
                                                                                                             cTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTTATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCCCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCAt                       <  1:365539/140‑1 (MQ=255)
                                                                                                              cggttatCAGGGTTTGACGGTATCAGCAGCCGTCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCAtt                      >  2:557611/7‑140 (MQ=14)
                                                                                                                aTTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATtca                    >  2:498871/1‑140 (MQ=255)
                                                                                                                  tGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATtcatc                  <  1:396674/140‑1 (MQ=255)
                                                                                                                          tttgacggTATCAGCAGCCGTCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTg          >  1:714379/7‑140 (MQ=14)
                                                                                                                          ttCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTg          >  2:113184/1‑140 (MQ=255)
                                                                                                                           ttgacggTATCAGCAGCCGTCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTgg         >  2:36889/6‑140 (MQ=14)
                                                                                                                            tgacggTATCAGCAGCCGTCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGa        >  1:75962/5‑140 (MQ=17)
                                                                                                                              aGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACg      >  2:597766/1‑140 (MQ=255)
                                                                                                                                 gTATCAGCAGCCGTCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGtt   >  1:419470/1‑140 (MQ=255)
                                                                                                                                  tATCAGCAGCCGTCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGttt  >  1:392933/1‑140 (MQ=255)
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GAACCCCGGGATAGCAGAGGCATTAAAGCTCGCGAGCAGTACACCCGCCAGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTT  >  NC_000913/266007‑266276

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑