Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,213,5740AT20.0% 55.5 / 11.3 25T244T (ACA→ACT) carBCarbamoyl‑phosphate synthase large chain
Reads supporting (aligned to +/- strand):  ref base A (8/12);  new base T (1/4);  total (9/16)
Fisher's exact test for biased strand distribution p-value = 6.21e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.23e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AGTCCAGCAACGCAATGTTTATTAGAAAAATCTATCGCAGGTTTTAAAGAAATCGAATACGAAGTAATGCGTGATAAAAACGATAATGCCATCGTTGTATGTAACATGGAAAATATTGATCCAGTTGGTATTCATACAGGCGATTCAATTGTTGTGGCTCCTAGTCAAACATTATCAGATGTTGAGTATCAAATGTTACGTGATGTTTCATTAAAAGTTATTCGAGCTTTAGGTATCGAAGGTGGTTGTAATGTTCAATTAGCATTAGATCCCCATT  >  USA300TCH1516_ALE/1213437‑1213713
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aGTCCATCAACGCAATGTTTATTAGAAAAATCTATCGCAGGTCTTAAAGAAATCGAATACGAAGTAATGCGTGATAAAAACGATAATGCCATCGTTGTATGTAACATGGAAAATATTGATCCAGTTGGTATTCATACAGGc                                                                                                                                          <  2:214773/141‑1 (MQ=255)
        aaCGCAATGTTTATTAGAAAAATCTATCGCAGGTTTTAAAGAAATCGAATACGAAGTAATGCGTGATAAAAACGATAATGCCATCGTTGTATGTAACATGGAAAATATTGATCCAGTTGGTATTCATACAGGCGATTCAAt                                                                                                                                  >  1:219866/1‑141 (MQ=255)
           gCAATGTTTATTAGAAAAATCTATCGCAGGTTTTAAAGAAATCGAATACGAAGTAATGCGTGATAAAAACGATAATGCCATCGTTGTATGTAACATGGAAAATATTGATCCAGTTGGTATTCATACAGGCGATTCAAttgt                                                                                                                               <  2:164850/141‑1 (MQ=255)
             aaTGTTTATTAGAAAAATCTATCGCAGGTTTTAAAGAAATCGAATACGAAGTAATGCGTGATAAAAACGATAATGCCATCGTTGTATGTAACATGGAAAATATTGATCCAGTTGGTATTCATACAGGCGATTCAAttgttg                                                                                                                             >  1:39935/1‑141 (MQ=255)
                 tttATTAGAAAAATCTATCGCAGGTTTTAAAGAAATCGAATACGAAGTAATGCGTGATAAAAACGATAATGCCATCGTTGTATGTAACATGGAAAATATTGATCCAGTTGGTATTCATACAGGCGATTCAATTGTTGTGGc                                                                                                                         >  2:134680/1‑141 (MQ=255)
                       aGAAAAATCTATCGCAGGTTTTAAAGAAATCGAATACGAAGTAATGCGTGATAAAAACGATAATGCCATCGTTGTATGTAACATGGAAAATATTGATCCAGTTGGTATTCATACTGGCGATTCAATTGTTGTGGCTCCTAg                                                                                                                   <  2:212689/141‑1 (MQ=255)
                       aGAAAAATCTATCGCAGGTTTTAAAGAAATCGAATACGAAGTAATGCGTGATAAAAACGATAATGCCATCGTTGTATGTAACATGGAAAATATTGATCCAGTTGGTATTCATACTGGCGATTCAATTGTTGTGGCTCCTAg                                                                                                                   <  2:159136/141‑1 (MQ=255)
                       aGAAAAATCTATCGCAGGTTTTAAAGAAATCGAATACGAAGTAATGCGTGATAAAAACGATAATGCCATCGTTGTATGTAACATGGAAAATATTGATCCAGTTGGTATTCATACTGGCGATTCAATTGTTGTGGCTCCTAg                                                                                                                   <  2:136471/141‑1 (MQ=255)
                       aGAAAAATCTATCGCAGGTTTTAAAGAAATCGAATACGAAGTAATGCGTGATAAAAACGATAATGCCATCGTTGTATGTAACATGGAAAATATTGATCCAGTTGGTATTCATACAGGCGATTCAATTGTTGTGGCTCCTAg                                                                                                                   >  2:67210/1‑141 (MQ=255)
                                 aTCGCAGGTTTTAAAGAAATCGAATACGAAGTAATGCGTGATAAAAACGATAATGCCATCGTTGTATGTAACATGGAAAATATTGATCCAGTTGGTATTCATACAGGCGATTCAATTGTTGTGGCTCCTGGTCAAACATTa                                                                                                         >  2:78000/1‑141 (MQ=255)
                                                      gAATACGAAGTAATGCGTGATAAAAACGATAATGCCATCGTTGTATGTAACATGGAAAATATTGATCCAGTTGGTATTCATACTGGCGATTCAATTGTTGTGGCTCCTAGTCAAACATTATCAGATGTTGAGTATCAAATg                                                                                    <  1:26132/141‑1 (MQ=255)
                                                            gAAGTAATGCGTGATAAAAACGATAATGCCATCGTTGTATGTAACATGGAAAATATTGATCCAGTTGGTATTCATACTGGCGATTCAATTGTTGTGGCTCCTAGTCAAACATTATCAGATGTTGAGTATCAAATGTTACGt                                                                              >  2:191632/1‑141 (MQ=255)
                                                                  aTGCGTGATAAAAACGATAATGCCATCGTTGTATGTAACATGGAAAATATTGATCCAGTTGGTATTCATACAGGCGATTCAATTGTTGTGGCTCCTAGTCAAACATTATCAGATGTTGAGTATCAAATGTTACGTGATGtt                                                                        <  1:31810/141‑1 (MQ=255)
                                                                             aaaCGATAATGCCATCGTTGTATGTAACATGGAAAATATTGATCCAGTTGGTATTCATACAGGCGATTCAATTGTTGTGGCTCCTAGTCAAACATTATCAGATGTTGAGTATCAAATGTTACGTGATGTTTCATTAAAAGt                                                             <  1:165350/141‑1 (MQ=255)
                                                                                  aTAATGCCATCGTTGTATGTAACATGGAAAATATTGATCCAGTTGGTATTCATACAGGCGATTCAATTGTTGTGGCTCCTAGTCAAACATTATCAGATGTTGAGTATCAAATGTTACGTGATGTTTCATTAAAAGTTATTc                                                        <  2:39935/141‑1 (MQ=255)
                                                                                                   tgtaACATGGAAAATATTGATCCAGTTGGTATTCATACAGGCGATTCAATTGTTGTGGCTCCTAGTCAAACATTATCAGATGTTGAGTATCAAATGTTACGTGATGTTTCATTAAAAGTTATTCGAGCTTTAGGTATCGaa                                       <  2:219866/141‑1 (MQ=255)
                                                                                                                   ttGATCCAGTTGGTATTCATACAGGCGATTCAATTGTTGTGGCTCCTAGTCAAACATTATCAGATGTTGAGTATCAAATGTTACGTGATGTTTCATTAAAAGTTATTCGAGCTTTAGGTATCGAAGGTGGTTGTAATGTTc                       >  2:94423/1‑141 (MQ=255)
                                                                                                                    tGATCCAGTTGGTATTCATACAGGCGATTCAATTGTTGTGGCTCCTAGTCAAACATTATCAGATGTTGAGTATCAAATGTTACGTGATGTTTCATTAAAAGTTATTCGAGCTTTAGGTATCGAAGGTGGTTGTAATGTTCa                      <  1:139344/141‑1 (MQ=255)
                                                                                                                        ccAGTTGGTATTCATACAGGCGATTCAATTGTTGTGGCTCCTAGTCAAACATTATCAGATGTTGAGTATCAAATGTTACGTGATGTTTCATTAAAAGTTATTCGAGCTTTAGGTATCGAAGGTGGTTGTAATGTTCAATTa                  <  1:134680/141‑1 (MQ=255)
                                                                                                                         cAGTTGGTATTCATACAGGCGATTCAATTGTTGTGGCTCCTAGTCAAACATTATCAGATGTTGAGTATCAAATGTTACGTGATGTTTCATTAAAAGTTATTCGAGCTTTAGGTATCGAAGGTGGTTGTAATGTTCAATTAg                 <  2:69986/141‑1 (MQ=255)
                                                                                                                          aGTTGGTATTCATACAGGCGATTCAATTGTTGTGGCTCCTAGTCAAACATTATCAGATGTTGAGTATCAAATGTTACGTGATGTTTCATTAAAAGTTATTCGAGCTTTAGGTATCGAAGGTGGTTGTAATGTTCAATTAGc                <  1:35980/141‑1 (MQ=255)
                                                                                                                          aGTTGGTATTCATACAGGCGATTCAATTGTTGTGGCTCCTAGTCAAACATTATCAGATGTTGAGTATCAAATGTTACGTGATGTTTCATTAAAAGTTATTCGAGCTTTAGGTATCGAAGGTGGTTGTAATGTTCAATTAGc                <  1:14472/141‑1 (MQ=255)
                                                                                                                              ggTATTCATACAGGCGATTCAATTGTTGTGGCTCCTAGTCAAACATTATCAGATGTTGAGTATCAAATGTTACGTGATGTTTCATTAAAAGTTATTCGAGCTTTAGGTATCGAAGGTGGTTGTAATGTTCAATTAGCATTa            >  2:1667/1‑141 (MQ=255)
                                                                                                                                    cATACAGGCGATTCAATTGTTGTGGCTCCTAGTCAAACATTATCAGATGTTGAGTATCAAATGTTACGTGATGTTTCATTAAAAGTTATTCGAGCTTTAGGTATCGAAGGTGGTTGTAATGTTCAATTAGCATTAGATccc      <  1:85949/141‑1 (MQ=255)
                                                                                                                                        cAGGCGATTCAATTGTTGTGGCTCCTAGTCAAACATTATCAGATGTTGAGTATCAAATGTTACGTGATGTTTCATTAAAAGTTATTCGAGCTTTAGGTATCGAAGGTGGTTGTAATGTTCAATTAGCATTAGATCCCcatt  >  2:191249/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                           
AGTCCAGCAACGCAATGTTTATTAGAAAAATCTATCGCAGGTTTTAAAGAAATCGAATACGAAGTAATGCGTGATAAAAACGATAATGCCATCGTTGTATGTAACATGGAAAATATTGATCCAGTTGGTATTCATACAGGCGATTCAATTGTTGTGGCTCCTAGTCAAACATTATCAGATGTTGAGTATCAAATGTTACGTGATGTTTCATTAAAAGTTATTCGAGCTTTAGGTATCGAAGGTGGTTGTAATGTTCAATTAGCATTAGATCCCCATT  >  USA300TCH1516_ALE/1213437‑1213713

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑