Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,284,2480TA31.2% 33.3 / 26.1 32S271S (TCT→TCA) polC_1DNA polymerase III PolC‑type
Reads supporting (aligned to +/- strand):  ref base T (10/12);  new base A (7/3);  total (17/15)
Fisher's exact test for biased strand distribution p-value = 2.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AAATATTAAACCAATTGAATCTATTATTGAGGAAGAGTTTAAAGTTGCAATAGAGGGTGTCATTTTTGATATAAACTTAAAAGAACTTAAAAGTGGTCGCCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCTTTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTTGGTAAATGGGTTAGGGCTCAAGGTCGTATTGAAGAAGATACATTTATTAGAGATTTAGTTATGATGATGTCT  >  USA300TCH1516_ALE/1284110‑1284386
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aaaTATTAAACCAATTGAATCTATTATTGAGGAAGAGTTTAAAGTTGCAATAGAGGGTGTCATTTTTGATATAAACTTAAAAGAACTTAAAAGTGGTCGCCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCttt                                                                                                                                          <  2:295050/141‑1 (MQ=255)
  atatTAAACCAATTGAATCTATTATTGAGGAAGAGTTTAAAGTTGCAATAGAGGGTGTCATTTTTGATATAAACTTAAAAGAACTTAAAAGTGGTCGTCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCATTAg                                                                                                                                        >  1:145223/1‑141 (MQ=255)
  atatTAAACCAATTGAATCTATTATTGAGGAAGAGTTTAAAGTTGCAATAGAGGGTGTCATTTTTGATATAAACTTAAAAGAACTTAAAAGTGGTCGTCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCATTAg                                                                                                                                        >  2:178685/1‑141 (MQ=255)
  atatTAAACCAATTGAATCTATTATTGAGGAAGAGTTTAAAGTTGCAATAGAGGGTGTCATTTTTGATATAAACTTAAAAGAACTTAAAAGTGGTCGTCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCATTAg                                                                                                                                        >  1:237318/1‑141 (MQ=255)
          cccaTTGAATCTCTTATTAAGGAAGTGTTTAAAGATGCATTAGAGGGTGTCATTTTTGATATAACCTTAAAAGAACTGAAAAGTGGCCGCCATATCGTAGAAATTGAAGTGACTGAGTATGAGGTCTATATAGATTTagaa                                                                                                                                >  2:38117/4‑141 (MQ=255)
           cAATTGAATCTATTATTGAGGAAGAGTTTAAAGTTGCAATAGAGGGTGTCATTTTTGATATAAACTTAAAAGAACTTAAAAGTGGTCGCCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCTTTAGTTTTaaaaa                                                                                                                               >  1:18210/1‑141 (MQ=255)
           cAATTGAATCTATTATTGAGGAAGAGTTTAAAGTTGCAATAGAGGGTGTCATTTTTGATATAAACTTAAAAGAACTTAAAAGTGGTCGCCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCTTTAGTTTTaaaaa                                                                                                                               >  1:29767/1‑141 (MQ=255)
            aaTTGAATCTATTATTGAGGAAGAGTTTAAAGTTGCAATAGAGGGTGTCATTTTTGATATAAACTTAAAAGAACTTAAAAGTGGTCGCCATATCGTAGAAATTAAAGCGACTGACTATACGGACTCTTTAGTTTTaaaaaa                                                                                                                              >  2:255626/1‑140 (MQ=255)
                                                      gggTGTCATTTTTGATATAAACTTAAAAGAACTTAAAAGTGGTCGCCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCTTTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAgc                                                                                    <  1:227820/141‑1 (MQ=255)
                                                        gtgtCATTTTTGATATAAACTTAAAAGAACTTAAAAGTGGTCGCCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCTTTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAgcgc                                                                                  <  2:320614/141‑1 (MQ=255)
                                                           tCATTTTTGAGATAAACTTAAGAGAACTTAAAAGTGGTCGCCATATCGTAGAAATTAAAGTGACTGACTATACGGACTGTTTAGTTTTAAAAAGGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTaa                                                                               <  1:23205/141‑1 (MQ=255)
                                                                  tGATATAAACTTATCAAAGCTTAAAAGTGGTCGCCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCTTTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTTgg                                                                        <  1:334234/141‑1 (MQ=255)
                                                                  tGATATAAACTTAAAAGAACTTAAAAGTGGTCGCCATATCGTAGAAATTAAAGTGTCTGACTATACGGACTCTTTAGTTTGAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTTgg                                                                        <  2:311530/141‑1 (MQ=255)
                                                                  tGATATAAACTTAAAAGAACTTAAAAGTGGTCGCCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCTTTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTTgg                                                                        <  1:253780/141‑1 (MQ=255)
                                                                    atatAAACTTAAAAGAACTTAAAAGTGGTCGCCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCTTTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTTGGTa                                                                      <  1:158673/141‑1 (MQ=255)
                                                                    atatAAACTTAAAAGAACTTAAAAGTGGTCGCCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCTTTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTTGGTa                                                                      <  1:88292/141‑1 (MQ=255)
                                                                             taaaagaacttaaaagTGGTCGCCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCTTTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTTGGTAAATGGGTTa                                                             <  1:93335/141‑1 (MQ=255)
                                                                               aaagaacttaaaagTGGTCGCCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCTTTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTTGGTAAATGGGTTAgg                                                           >  1:244219/1‑141 (MQ=255)
                                                                                 agaacttaaaagTGGTCGCCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCTTTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTTGGTAAATGTGTTAGGGc                                                         >  1:63908/1‑141 (MQ=255)
                                                                                       taaaagTGGTCGTCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCATTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTAGGTAAATGGGTTAGGGCTCAAgg                                                   >  1:82133/1‑141 (MQ=255)
                                                                                       taaaagTGGTCGTCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCATTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTAGGTAAATGGGTTAGGGCTCAAgg                                                   >  1:403736/1‑141 (MQ=255)
                                                                                       taaaagTGGTCGTCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCATTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTAGGTAAATGGGTTAGGGCTCAAgg                                                   >  1:175277/1‑141 (MQ=255)
                                                                                       taaaagTGGTCGCCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCTTTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTTGGTAAATGGGTTAGGGCTCAAgg                                                   >  1:147707/1‑141 (MQ=255)
                                                                                                   ccATATCGTAGAAATTAAAGTGACTGACTATACTGACTCTGGAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTTGGTAAATGGGTTAGGGCTCAAGGTCGTATTgaaga                                       >  2:226808/1‑141 (MQ=255)
                                                                                                      tatCGTANAAATTAAATTTACTTACTTTACGGACTCTTTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATTATTTAGAACATTTGAAAGCGTTAATTTTTTTTAAATTGGTTATGTCTCAAGGTCGTATTGAagaaga                                    <  2:309947/141‑1 (MQ=255)
                                                                                                        tCGTAGAAATTAAAGTGACTGACTATACGGACTCATTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTAGGTAAATGGGTTAGGGCTCAAGGTCGTATTGAAGAAGATa                                  <  2:145223/141‑1 (MQ=255)
                                                                                                        tCGTAGAAATTAAAGTGACTGACTATACGGACTCATTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTAGGTAAATGGGTTAGGGCTCAAGGTCGTATTGAAGAAGATa                                  <  2:237318/141‑1 (MQ=255)
                                                                                                        tCGTAGAAATTAAAGTGACTGACTATACGGACTCATTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTAGGTAAATGGGTTAGGGCTCAAGGTCGTATTGAAGAAGATa                                  <  1:178685/141‑1 (MQ=255)
                                                                                                                   aaaGTGACAGACTATACTGACTCATTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTTGGTAAATGGGTTAGGGCTCAAGGTCGTATTGAAGAAGATACATTTATTaga                       >  2:357577/1‑141 (MQ=255)
                                                                                                                       tgactgacTATACGGACTCTTTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTTGGTAAATGGGTTAGGGCCCAAGGTCGTCTCGAAGAAGATACATCTATTACGGAtt                   >  2:213853/1‑141 (MQ=255)
                                                                                                                           tgactATACGGACTCTTTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTTGGTAAATGGGTTAGGGCTCAAGGTCGTATTGAAGAAGATACATTTATTAGAGATTTAGt               <  1:259471/141‑1 (MQ=255)
                                                                                                                                  aCGGACTCTTTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTAGGTAAATGGGTTAGGGCTCAAGGGCGTATTGAAGAAGATACATTTATTAGAGATTTAGTTatgatg        >  1:123670/1‑141 (MQ=255)
                                                                                                                                   cGGACTCTTTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTTGGTAAATGGGTTAGGGCTCAAGGTCGTATTGAAGAAGATACATTTATTAGAGATTTAGTTatgatga       <  1:409172/141‑1 (MQ=255)
                                                                                                                                        tctTTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTTGGTAAATGTGTTAGGGCTCAAGGTCGTATTGAAGAAGATACATTTATTAGAGATTTAGTTATGATGATGTCt  <  2:63908/141‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                          
AAATATTAAACCAATTGAATCTATTATTGAGGAAGAGTTTAAAGTTGCAATAGAGGGTGTCATTTTTGATATAAACTTAAAAGAACTTAAAAGTGGTCGCCATATCGTAGAAATTAAAGTGACTGACTATACGGACTCTTTAGTTTTAAAAATGTTTACTCGTAAAAACAAAGATGATTTAGAACATTTTAAAGCGCTAAGTGTTGGTAAATGGGTTAGGGCTCAAGGTCGTATTGAAGAAGATACATTTATTAGAGATTTAGTTATGATGATGTCT  >  USA300TCH1516_ALE/1284110‑1284386

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑