Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE512,6430AG50.0% ‑6.0 / 62.9 42intergenic (+711/‑6052)recR/speA_2Recombination protein RecR/Arginine decarboxylase
Reads supporting (aligned to +/- strand):  ref base A (18/3);  new base G (14/7);  total (32/10)
Fisher's exact test for biased strand distribution p-value = 2.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TGTAATTTTTACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTTATGAGCTAATCAAACATCATAA  >  USA300TCH1516_ALE/512506‑512783
                                                                                                                                         |                                                                                                                                            
tgtAATTTTTACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTtaata                                                                                                                                           >  2:16593/1‑141 (MQ=255)
       aagctccttagcgtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagtttttttttttatttttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGta                                                                                                                                    <  2:194187‑M1/34‑1 (MQ=255)
            ccttagcgtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTAtaatt                                                                                                                               >  1:34534‑M1/103‑141 (MQ=255)
              ttagcgtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTAtaattaa                                                                                                                             >  1:75207‑M1/101‑141 (MQ=255)
                 gcgtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTc                                                                                                                          <  1:138667‑M1/44‑1 (MQ=255)
                      gatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTc                                                                                                                     >  2:187630‑M1/93‑141 (MQ=255)
                      gatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTc                                                                                                                     >  1:225146‑M1/93‑141 (MQ=255)
                            agtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAg                                                                                                               >  1:196447‑M1/87‑141 (MQ=255)
                            agtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAg                                                                                                               <  2:210982‑M1/55‑1 (MQ=255)
                                gCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAGTGTATAATTAATTCTTGTCGGTAAGaaaa                                                                                                           >  1:114363/1‑141 (MQ=255)
                                gCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGaaaa                                                                                                           >  1:168727/1‑141 (MQ=255)
                                gCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGaaaa                                                                                                           >  1:114367/1‑141 (MQ=255)
                                      ataGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAAc                                                                                                     >  2:86824/1‑141 (MQ=255)
                                      acgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTATTGCCAGGAAGAAAAATGAAc                                                                                                     <  1:12375‑M1/65‑1 (MQ=255)
                                       cgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACa                                                                                                    <  2:108554‑M1/66‑1 (MQ=255)
                                                           aaacaaaacaACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAata                                                                                <  2:61689/141‑1 (MQ=255)
                                                             acaaaacaaCTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATg                                                                              >  2:102835/1‑141 (MQ=255)
                                                                  acaacTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAAc                                                                         >  1:3996/1‑141 (MQ=255)
                                                                  acaacTCAACTTAAGAAATAACTTGAATTACTAACGAAAAGTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAAc                                                                         >  1:89591/1‑141 (MQ=255)
                                                                     actcaactTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGtt                                                                      >  1:106328/1‑141 (MQ=255)
                                                                     actcaactTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGtt                                                                      >  2:4523/1‑141 (MQ=255)
                                                                               aGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCaaaa                                                            >  1:185922/1‑141 (MQ=255)
                                                                                aaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCaaaaa                                                           >  1:63319‑M1/35‑141 (MQ=255)
                                                                                 aaaTAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCaaaaaa                                                          >  2:2916/1‑141 (MQ=255)
                                                                                 aaaTAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCaaaaaa                                                          >  2:214499/1‑141 (MQ=255)
                                                                                       cTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAAc                                                    >  2:197331/1‑141 (MQ=255)
                                                                                        ttGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACt                                                   <  1:16593/141‑1 (MQ=255)
                                                                                                   aaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACaa                                        >  1:90583‑M1/16‑141 (MQ=255)
                                                                                                   aaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACaa                                        >  2:215216‑M1/16‑141 (MQ=255)
                                                                                                   aaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAA‑CGTAACTATAAGTTACaaa                                       >  1:108554‑M1/16‑141 (MQ=255)
                                                                                                         attaattTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACatta                                  >  2:175862/1‑141 (MQ=255)
                                                                                                             attTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTa                              >  2:179743/1‑141 (MQ=255)
                                                                                                                       gatATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTTATGa                    >  2:6719/3‑141 (MQ=255)
                                                                                                                       gTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTTATGa                    >  2:74174/1‑141 (MQ=255)
                                                                                                                        ttATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTTATGAg                   <  2:185922/141‑1 (MQ=255)
                                                                                                                            tGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTTATGAGCTaa               <  1:210982/141‑1 (MQ=255)
                                                                                                                             gACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAAAGATAATAAAAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTTATGAGCTAAt              <  2:135531/141‑1 (MQ=21)
                                                                                                                               cTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTTATGAGCTAATCa            >  2:146650/1‑141 (MQ=255)
                                                                                                                               cTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTTATGAGCTAATCa            >  2:84344/1‑141 (MQ=255)
                                                                                                                                ttAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTTATGAGCTAATCaa           >  2:180897/1‑141 (MQ=255)
                                                                                                                                ttAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTTATGAGCTAATCaa           >  2:137794/1‑141 (MQ=255)
                                                                                                                                  aattGTTGATAAAATGTATAATTAATTCTTGTCGGTTAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCTAAAAAACGTAACTATAAGTAACAAACAATATTTAGTATTTTTAAGCTAATCaaaa         >  2:150269/4‑140 (MQ=18)
                                                                                                                                       ttAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTTATGAGCTAATCAAAcatcat    >  1:159879/1‑141 (MQ=255)
                                                                                                                                         aataaAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTTATGAGCTAATCAAACATCATaa  >  2:191331/1‑141 (MQ=255)
                                                                                                                                         aataaAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTTATGAGCTAATCAAACATCATaa  >  2:108926/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                            
TGTAATTTTTACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTTATGAGCTAATCAAACATCATAA  >  USA300TCH1516_ALE/512506‑512783

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: ‑