Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,026,6550CT40.0% 14.4 / 37.6 35E87K (GAA→AAA) vraRresponse regulator VraR
Reads supporting (aligned to +/- strand):  ref base C (12/9);  new base T (2/12);  total (14/21)
Fisher's exact test for biased strand distribution p-value = 1.56e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.16e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AAACTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATGGGCTTTGGCAATT  >  CP000730/2026523‑2026794
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aaaCTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGTACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAAc                                                                                                                                     <  2:391075/141‑1 (MQ=255)
 aaCTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACt                                                                                                                                    <  1:308134/141‑1 (MQ=255)
  aCTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACtg                                                                                                                                   <  2:196737/141‑2 (MQ=255)
  aCTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTa                                                                                                                                   <  2:18816/141‑1 (MQ=255)
     tCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCTATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGtt                                                                                                                                <  1:88364/141‑1 (MQ=255)
      ccGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTa                                                                                                                               >  1:175013/1‑141 (MQ=255)
       cGGTTCAAAAACAGATTTTCCTCTAGAAGTTTTACGAACTGCATCGGAGTTATCTTTTGTATTTGTTGTTTTTAATATGTTATTATTTACACCTGCATATTATTCACGTTATACCTATTTATCTTCATTTAAAATATTTaa                                                                                                                              >  2:96858/1‑141 (MQ=255)
       cGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTaa                                                                                                                              >  2:4138/1‑141 (MQ=255)
        ggTTAAAAAACAGATTCTCCTCTAGTAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAAc                                                                                                                             <  1:12214/141‑1 (MQ=255)
                    gATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTa                                                                                                                 <  2:81587/141‑1 (MQ=255)
                    gATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTGTa                                                                                                                 >  1:252632/1‑141 (MQ=255)
                      ttCTCCTCTAGCAGTTTCACTAACTGCATCGGCGACATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAACGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTact                                                                                                               <  2:421438/141‑3 (MQ=255)
                        ctcctcTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAAttt                                                                                                             >  1:234703/1‑141 (MQ=255)
                            tctAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATTCCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCgg                                                                                                         <  2:106476/141‑1 (MQ=255)
                            tctAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCgg                                                                                                         >  2:163890/1‑141 (MQ=255)
                                gAAGTTTTACGAACTGCATCGCCGATTTCGTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTaaa                                                                                                     >  1:200270/1‑141 (MQ=255)
                                  aGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATc                                                                                                   <  1:73189/141‑1 (MQ=255)
                                      ttACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCtttt                                                                                               <  1:307986/141‑1 (MQ=255)
                                         cGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTa                                                                                            <  2:242860/141‑1 (MQ=255)
                                         cGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTa                                                                                            >  1:131279/1‑141 (MQ=255)
                                             cTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCt                                                                                        <  1:5670/141‑1 (MQ=255)
                                             cTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCt                                                                                        <  1:5687/141‑1 (MQ=255)
                                                                                   aTGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGt                                                  <  1:163890/141‑1 (MQ=255)
                                                                                    tGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTa                                                 >  2:147921/1‑141 (MQ=255)
                                                                                    tGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTa                                                 >  2:117278/1‑141 (MQ=255)
                                                                                                        tCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGATTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCt                             >  2:87762/1‑141 (MQ=255)
                                                                                                            aTGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCt                         >  2:69435/1‑141 (MQ=255)
                                                                                                                   atatACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTc                  <  1:328818/141‑1 (MQ=255)
                                                                                                                   atatACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTc                  <  1:224800/141‑1 (MQ=255)
                                                                                                                    tataCCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCa                 <  1:318426/141‑1 (MQ=255)
                                                                                                                    tataCCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCa                 <  1:387889/141‑1 (MQ=255)
                                                                                                                    tataCCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCa                 <  2:132533/141‑1 (MQ=255)
                                                                                                                     ataCCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCAt                <  1:138098/141‑1 (MQ=255)
                                                                                                                            tttATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATGGGCttt         >  2:365681/1‑141 (MQ=255)
                                                                                                                                   tCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTTTTTTTTTTCTTCGCTTATACAGCATACATGTCATCCATAAGTAACTCCATTAAAATTAAATCTGGCTTCAACCCATATGCTTTTGCCAtt  >  2:368730/1‑141 (MQ=255)
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AAACTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATGGGCTTTGGCAATT  >  CP000730/2026523‑2026794

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑