Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,646,1290GA25.7% 65.6 / 15.3 35A175V (GCA→GTA) ypdFAminopeptidase YpdF
Reads supporting (aligned to +/- strand):  ref base G (13/13);  new base A (4/5);  total (17/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01
Rejected as consensus: Frequency below/above cutoff threshold.

ATAATACGCGCCAAAATCTAATGTAATCATGTCGCCTTTTTCAATAATTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTT  >  USA300TCH1516_ALE/1646005‑1646273
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ataataCGCGCCAAAATCTAATGTAATCATGTCGCCTTTTTCAATAATTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCtt                                                                                                                           <  2:382333/148‑1 (MQ=255)
      cgcgCCAAAATCTAATGTAATCATGTCGCCTTTTTTTTTTTTTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCTAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAat                                                                                                                     >  2:362891/1‑148 (MQ=255)
      cgcgCCAAAATCTAATGTAATCATGTCGCCTTTTTCAATAATTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAat                                                                                                                     >  2:95434/1‑148 (MQ=255)
      cgcgCCAAAATCTAATGTAATCATGTCGCC‑TTTTCAATAATTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAata                                                                                                                    >  2:303104/1‑148 (MQ=255)
                    aTGTAATCATGTCGCCTTTTTCAATAATTTTATCACTTGCAACACCATGTTGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTc                                                                                                       <  2:317063/148‑1 (MQ=255)
                                cGCCTTTTTCAATAATTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTACTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCAt                                                                                           >  1:114177/1‑148 (MQ=255)
                                cGCCTTTTTCAATAATTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTACTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCAt                                                                                           >  2:320497/1‑148 (MQ=255)
                                cGCCTTTTTCAATAATTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTACTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCAt                                                                                           >  1:345106/1‑148 (MQ=255)
                                cGCCTTTTTCAATAATTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTACTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCAt                                                                                           >  1:315027/1‑148 (MQ=255)
                                    tttttCAATAATTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCt                                                                                       <  1:381328/148‑1 (MQ=255)
                                    tttttCAATAATTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCt                                                                                       <  1:118968/148‑1 (MQ=255)
                                         cAATAATTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCttt                                                                                  <  1:269405/148‑1 (MQ=255)
                                         cAATAATTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCttt                                                                                  <  1:213119/148‑1 (MQ=255)
                                                 ttATCACTTGCAACACCATGTGGTAATGCGCCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAg                                                                          >  2:75650/1‑148 (MQ=255)
                                                 ttATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAg                                                                          >  2:351297/1‑148 (MQ=255)
                                                           cAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAatata                                                                <  1:183050/148‑1 (MQ=255)
                                                            aaCACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAatatat                                                               >  1:118642/1‑148 (MQ=255)
                                                            aaCACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAatatat                                                               >  2:277660/1‑148 (MQ=255)
                                                            aaCACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAatatat                                                               >  1:134546/1‑148 (MQ=255)
                                                            aaCACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAatatat                                                               >  2:102149/1‑148 (MQ=255)
                                                            aaCACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAatatat                                                               >  1:65445/1‑148 (MQ=255)
                                                                ccATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCat                                                           <  2:118683/148‑1 (MQ=255)
                                                                      ggTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGttt                                                     >  1:350482/1‑148 (MQ=255)
                                                                                    aTGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTa                                       <  2:317028/148‑1 (MQ=255)
                                                                                          aGATGCTACACTCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCATTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctgct                                 >  2:388755/1‑148 (MQ=255)
                                                                                                    aTCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTa                       <  2:148388/148‑1 (MQ=255)
                                                                                                    aTCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTa                       <  2:229991/148‑1 (MQ=255)
                                                                                                    aTCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTa                       <  2:350126/148‑1 (MQ=255)
                                                                                                                     tCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTGAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCa      <  2:205908/148‑1 (MQ=255)
                                                                                                                     tCCATCTACTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCa      <  2:345106/148‑1 (MQ=255)
                                                                                                                     tCCATCTACTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCa      <  1:84488/148‑1 (MQ=255)
                                                                                                                     tCCATCTACTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCa      <  2:315027/148‑1 (MQ=255)
                                                                                                                     tCCATCTACTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCa      <  1:320497/148‑1 (MQ=255)
                                                                                                                     tCCATCTACTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCATTTTCAGTCATGTCGACCTTTACAACAGTTAAAATATAGTCATATGTTTAATCACCAATATCAGCTGCTTTTTGAAATAAAGCAATTTCGTCAGCa      <  2:114177/148‑1 (MQ=255)
                                                                                                                         tCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCtt  >  1:332028/1‑148 (MQ=255)
                                                                                                                            |                                                                                                                                                
ATAATACGCGCCAAAATCTAATGTAATCATGTCGCCTTTTTCAATAATTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTT  >  USA300TCH1516_ALE/1646005‑1646273

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑