Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE658,0550AT35.3% 13.6 / 11.4 17L157F (TTA→TTT) USA300HOU_RS03150hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (8/3);  new base T (2/4);  total (10/7)
Fisher's exact test for biased strand distribution p-value = 1.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.80e-01
Rejected as consensus: Frequency below/above cutoff threshold.

ACATTTTATGTACGCCTAATTAAAAAATCATCTTTAAATATTTATAATACTAAAAATAAAAGGTCAAAAATTATCTTAATACCAACACTAAAAAATTTTTGTTTAACATTGTTTAGATATGCTTTTTTTATTTTATGGACAGTGATTTTCTCATATGCTCTATTATCAATGAGTTATCAAAACATAATAGTATATTTTGCTTGGATTACAGCAATAATGGGTTTTTTTCTAGTGAATATAGCTTTAATTATAGAT  >  USA300TCH1516_ALE/657921‑658175
                                                                                                                                      |                                                                                                                        
aCATTTTATGTACGCCTAATTAAAAAATCATCTTTAAATATTTATAATACTAAAAATAAAAGGTCAAAAATTATCTTAATACCAACACTAAAAAATTTTTGTTTAACATTGTTTAGATATGCTTTTTTTATTTTATGGACa                                                                                                                    >  2:301333/1‑141 (MQ=255)
       aTGTACGCCTAATTAAAAAATCATCTTTAAATATTTATAATACTAAAAATAAAAGGTCAAAAATTATCTTAATACCAACACTAAAAAATTTTTGTTTAACATTGTTTAGATATGCTTTTTTTATTTTATGTACAGTGAttt                                                                                                             >  2:272684/1‑141 (MQ=255)
       aTGTACGCCTAATTAAAAAATCATCTTTAAATATTTATAATACTAAAAATAAAAGGTCAAAAATTATCTTAATACCAACACTAAAAAATTTTTGTTTAACATTGTTTAGATATGCTTTTTTTATTTTATGGACAGTGAttt                                                                                                             >  2:187334/1‑141 (MQ=255)
            cGCCTAATTAAAAAATCATCTTTAAATATTTATAATACTAAAAATAAAAGGTCAAAAATTATCTTAATACCAACACTAAAAAATTTTTGTTTAACATTGTTTAGATATGCTTTTTTTATTTTATGGACAGTGATTTTCTCa                                                                                                        >  2:93280/1‑141 (MQ=255)
            cGCCTAATTAAAAAATCATCTTTAAATATTTATAATACTAAAAATAAAAGGTCAAAAATTATCTTAATACCAACACTAAAAAATTTTTGTTTAACATTGTTTAGATATGCTTTTTTTATTTTATGGACAGTGATTTTCTCa                                                                                                        >  2:336276/1‑141 (MQ=255)
            cGCCTAATTAAAAAATCATCTTTAAATATTTATAATACTAAAAATAAAAGGTCAAAAATTATCTTAATACCAACACTAAAAAATTTTTGTTTAACATTGTTTAGATATGCTTTTTTTATTTTATGGACAGTGATTTTCTCa                                                                                                        >  2:162909/1‑141 (MQ=255)
                      aaaaaTCATCTTTAAATATTTATAATACTAAAAATAAAAGGTCGAAAATCATCTTAATACCAACACTAAAAAATTTTTGTTTCACATTGTTCGGATATGTTTTTTTAATTTTTTGGACAGTGATTTTCTCATATGCTCtat                                                                                              <  2:113674/141‑1 (MQ=18)
                      aaaaaTCATCTTTAAATATTTATAATACTAAAAATAAAAGGTCGAAAATCATCTTAATACCAACACTAAAAAATTTTTGTTTCACATTGTTCGGATATGTTTTTTTAATTTTTTGGACAGTGATTTTCTCATATGCTCtat                                                                                              <  2:197233/141‑1 (MQ=18)
                       aaaaTCATCTTTAAATATTTATAATACTAAAAATAAAAGGTCAAAAATTATCTTAATACCAACACTAAAAAATTTTTGTTTAACATTGTTTAGATATGCTTTTTTTATTTTATGGACAGTGATTTTCTCATATGCTGtatt                                                                                             >  1:271776/1‑141 (MQ=255)
                                   aaaTATTTATAATACTAAAAATAAAAGGTCAAAAATTATCTTAATACCAACACTAAAAAATTTTTGTTTAACATTGTTTAGATATGCTTTTTTTATTTTATGGACAGTGATTTTCTCATATGCTCTATTATCAATGAGTTa                                                                                 <  2:194411/141‑1 (MQ=255)
                                       atTTATAATACTAAAAATAAAAGGTCGAAAATCATCTTAATACCAACACTAAAAAATTTTTGTTTCACATTGTTCGGATATGTTTTTTTAATTTTTTGGACAGTGATTTTCTCATATGCTCTATTATCAATGAGTTATCaa                                                                             <  1:96536/141‑1 (MQ=25)
                                       atTTATAATACTAAAAATAAAAGGTCGAAAATCATCTTAATACCAACACTAAAAAATTTTTGTTTCACATTGTTCGGATATGTTTTTTTAATTTTTTGGACAGTGATTTTCTCATATGCTCTATTATCAATGAGTTATCaa                                                                             <  1:27807/141‑1 (MQ=25)
                                                                          cTTAATACCAACACTAAAAAATTTTTGTTTAACATTGTTTAGATATGCTTTTTTTATTTTATGGACAGTGATTTTCTCATATGCTCTATTATCAATGAGTTATCAAAACATAATAGTATATTTTGCTTGGATTAAAGCaat                                          >  2:113453/1‑141 (MQ=255)
                                                                                        taataaATTTTTGTTTAACATTGTTTAGATATGCTTTTTTTATTTTATGGACAGTGATTTTCTCATATGCTCTATTATCAATGAGTTATCAAAACATAATAGTATATTTTGCTTGGATTACAGCAATAATGGGTTTTTTTc                            <  1:309098/141‑1 (MQ=255)
                                                                                                            ttGTTTAGATATGCTTTTTTTATTTTATGGACAGTGATTTTCTCATATGCCCTATTATCAATGAGTTATCAAAACATAATAGTATATTTTGCTTGGATTACAGCAATAATGGGTTTTTTTCTAGTGAATATAGCTTTAAtt        <  2:293700/141‑1 (MQ=255)
                                                                                                                 tAGATATGCTTTTTTTTTTTTTTTTACAGTGATTTTCTCATATGCTCTATTATCAATGAGTTATCAAAACATAATAGTATATTTTGCTTGGATTACAGCAATAATGGGTTTTTTTCTAGTGAATATAGCTTTAATTATAGa   >  2:30646/1‑141 (MQ=255)
                                                                                                                  ggATATGTTTTTTTAATTTTTTGGACAGTGATTTTCTCATATGCTCTATTATCAATGAGTTATCAAAACATAATAGTATATTTTGCTTGGATTACAGCAATAATGGGTTTTTTTCTAGTGAATATAGCTTTAATTATAGAt  >  1:274770/2‑141 (MQ=255)
                                                                                                                                      |                                                                                                                        
ACATTTTATGTACGCCTAATTAAAAAATCATCTTTAAATATTTATAATACTAAAAATAAAAGGTCAAAAATTATCTTAATACCAACACTAAAAAATTTTTGTTTAACATTGTTTAGATATGCTTTTTTTATTTTATGGACAGTGATTTTCTCATATGCTCTATTATCAATGAGTTATCAAAACATAATAGTATATTTTGCTTGGATTACAGCAATAATGGGTTTTTTTCTAGTGAATATAGCTTTAATTATAGAT  >  USA300TCH1516_ALE/657921‑658175

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: ‑