Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,425,4540GA26.9% 41.4 / 14.2 26I272I (ATC→ATT) pstSPhosphate‑binding protein PstS
Reads supporting (aligned to +/- strand):  ref base G (9/10);  new base A (3/4);  total (12/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.94e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TCAGATTTCTTGTCGTCTGATTTTTGATTTTTATCAATAAATGCTTTTAAATCATCTAATTGTGATTTGTATGTTTTCTCTGGTGCTGCTACATATCCAGCTTCTTCAGCTGCTTTACCTTTATCTTCTAAGACGAATTTGATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATAAATGAATAATGGTCTACTTAATGCATAAGAGTTATCTTGAATTGTTTTTTTCGTAGGCTCTGTTGCTTTACCATTTTCATCTTTGATTTT  >  USA300TCH1516_ALE/1425314‑1425594
                                                                                                                                            |                                                                                                                                            
tcaGATTTCTTGTCGTCTGATTTTTGATTTTTATCAATAAATGCTTTTAAATCATCTAATTGTGATTTGTATGTTTTCTCTGGTGCTGCTACATATCCAGCTTCTTCAGCTGCTTTACCCTTATCTTCTAAGACGAATTTg                                                                                                                                              >  1:2476/1‑141 (MQ=255)
           gtcgtcTGATTTTTGATTTTTATCAATAAATGCTTTTAAATCATCTAATTGTGATTTGTATGTTTTCTCTGGTGCTGCTACATATCCAGCTTCTTCAGCTGCTTTACCTTTATCTTCTAAGACGAATTTAATAAATTCTGa                                                                                                                                   >  1:109274/1‑141 (MQ=255)
           gtcgtcTGATTTTTGATTTTTATCAATAAATGCTTTTAAATCATCTAATTGTGATTTGTATGTTTTCTCTGGTGCTGCTACATATCCAGCTTCTTCAGCTGCTTTACCTTTATCTTCTAAGACGAATTTAATAAATTCTGa                                                                                                                                   >  1:98063/1‑141 (MQ=255)
           gtcgtcTGATTTTTGATTTTTATCAATAAATGCTTTTAAATCATCTAATTGTGATTTGTATGTTTTCTCTGGTGCTGCTACATATCCAGCTTCTTCAGCTGCTTTACCTTTATCTTCTAAGACGAATTTAATAAATTCTGa                                                                                                                                   >  1:264669/1‑141 (MQ=255)
                  gatttttgatttttATCAATAAATGCTTTTAAATCATCTAATTGTGATTTGTATGTTTTCTCTGGTGCTGCTACATATCCAGCTTCTTCAGCTGCTTTACCTTTATCTTCTAAGACGAATTTGATAAATTCTGACATTACt                                                                                                                            <  1:253256/141‑1 (MQ=255)
                                aTCAATAAATGCTTTTAAATCATCTAATTGTGATTTGTATGTTTTCTCTGGTGCTGCTACATATCCAGCTTCTTCAGCTGCTTTACCTTTATCTTCTAAGACGAATTTGATAAATTCTGACATTACTTTATTATCTTTCaa                                                                                                              <  1:14535/141‑1 (MQ=255)
                                   aaTAAATGCTTTTAAATCATCTAATTGTGATTTGTATGTTTTCTCTGGTGCTGCTACATATCCAGCTTCTTCAGCTGCTTTACCTTTATCTTCTAAGACGAATTTGATAAATTCTGACATTACTTTATTATCTTTCAATGc                                                                                                           >  1:14007/1‑141 (MQ=255)
                                              ttAAATCATCTAATTGTGATTTGTATGTTTTCTCTGGTGCTGCTACATATCCAGCTTCTTCAGCTGCTTTACCTTTATCTTCTAAGACGAATTTGATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTa                                                                                                >  1:229138/1‑141 (MQ=255)
                                                  atcatcTAATTGTGATTTGTATGTTTTCTCTTGTGCTGCTACATATCCAGCTTCTTCAGCTGCTTTACCTTTATCTTCTAAGACGAATTTGATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATa                                                                                            >  2:149504/1‑141 (MQ=255)
                                                              tgATTTGTATGTTTTCTCTGGTGCTGCTACATATCCAGCTTCTTCAGCTGCTTTACCTTTATCTTCTAAGACGAATTTGATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATAAATGAATAATgg                                                                                <  2:75522/141‑1 (MQ=255)
                                                                 tttGTATGTTTTCTCTGGTGCTGCTACATATCCAGCTTCTTCAGCTGCTTTACCTTTATCTTCTAAGACGAATTTGATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATAAATGAATAATGGTCt                                                                             <  2:53431/141‑1 (MQ=255)
                                                                              tctGGTGCTGCTACATATCCAGCTTCTTCAGCTGCTTTACCTTTATCTTCTAAGACGAATTTGATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATAAATGAATAATGGTCTACTTAATGCATaa                                                                >  2:63364/1‑141 (MQ=255)
                                                                                            atatCCAGCTTCTTCAGCTGCTTTACCTTTATCTTCTAAGACGAATTTGATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATAAATGAATAATGGTCTACTTAATGCATAAGAGTTATCTTGAAt                                                  <  2:38996/141‑1 (MQ=255)
                                                                                            atatCCAGCTTCTTCAGCTGCTTTACCTTTATCTTCTAAGACGAATTTGATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATAAATGAATAATGGTCTACTTAATGCATAAGAGTTATCTTGAAt                                                  <  1:97834/141‑1 (MQ=255)
                                                                                            atatCCAGCTTCTTCAGCTGCTTTACCTTTATCTTCTAAGACGAATTTAATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATAAATGAATAATGGTCTACTTAATGCATAAGAGTTATCTTGAAt                                                  <  2:98063/141‑1 (MQ=255)
                                                                                            atatCCAGCTTCTTCAGCTGCTTTACCTTTATCTTCTAAGACGAATTTAATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATAAATGAATAATGGTCTACTTAATGCATAAGAGTTATCTTGAAt                                                  <  2:264669/141‑1 (MQ=255)
                                                                                            atatCCAGCTTCTTCAGCTGCTTTACCTTTATCTTCTAAGACGAATTTAATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATAAATGAATAATGGTCTACTTAATGCATAAGAGTTATCTTGAAt                                                  <  2:109274/141‑1 (MQ=255)
                                                                                              atCCAGCTTCTTCAGCTGCTTTACCTTTATCTTCTAAGACGAATTTGATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATAAATGAATAATGGTCTACTTAATGCATAAGAGTTATCTTGAATTg                                                <  1:6938/141‑1 (MQ=255)
                                                                                                          cAGCTGCTTTACCTTTATCTTCTAAGACGAATTTGATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATAAATGAATAATGGTCTACTTAATGCATAAGAGTTATCTTGAATTGTTTTTTTCGTAg                                    >  2:251283/1‑141 (MQ=255)
                                                                                                          cAGCTGCTTTACCTTTATCTTCTAAGACGAATTGGATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATAAATGAATAATGGTCTACTTAATGCATAAGAGTTATCTTGAATTGTTTTTTTCGTAg                                    >  1:158084/1‑141 (MQ=255)
                                                                                                                    aCCTTTATCTTCTAAGACGAATTTGATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATAAATGAATAATGGTCTACTTAATGCATAAGAGTTATCTTGAATTGTTTTTTTCGTAGGCTCTGTTGc                          >  1:8984/1‑141 (MQ=255)
                                                                                                                      cTTTATCTTCTAAGACGTAGACAATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATAAATGAATAATGGTCTACTTAATGCATAAGAGTTATCTTGAATTGTTTTTTTCGTAGGCTCTGTTGCtt                        <  1:2759/141‑1 (MQ=255)
                                                                                                                      cTTTATCTTCTAAGACGAATTTGATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATAAATGAATAATGGTCTACTTAATGCATAAGAGTTATCTTGAATTGTTTTTTTCGTAGGCTCTGTTGCtt                        <  1:189615/141‑1 (MQ=255)
                                                                                                                            cttctAAGACGAATTTGATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATAAATGAATAATGGTCTACTTAATGCATAAGAGTTATCTTGAATTGTTTTTTTCGTAGGCTCTGTTGCTTTACCAt                  <  2:277274/141‑1 (MQ=255)
                                                                                                                               ctAAGACGAATTTGATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCCTTTACATAAATGAATAATGGTCTACTTAATGCATAAGAGTTATCTTGAATTGTTTTTTTCGTAGGCTCTGTTGCTTTACCAtttt               <  1:8764/141‑1 (MQ=255)
                                                                                                                                      gAATTTGATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATAAATGAATAATGGTCTACTTAATGCATAAGAGTTATCTTGAATTGTTTTTTTCGTAGGCTCTGTTGCTTTACCATTTTCATCttt        >  2:109390/1‑141 (MQ=255)
                                                                                                                                      gAATTTGATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATAAATGAATAATGGTCTACTTAATGCATAAGAGTTATCTTGAATTGTTTTTTTCGTAGGCTCTGTTGCTTTACCATTTTCATCttt        >  2:261755/1‑141 (MQ=255)
                                                                                                                                            gATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATAAATGAATAATGGTCTACTTAATGCATAAGAGTTATCTTGAATTGTTTTTTTTGTTTTTTTTGTTGCTTTACCATTTTCATCTTTGAtttt  >  2:164311/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                            
TCAGATTTCTTGTCGTCTGATTTTTGATTTTTATCAATAAATGCTTTTAAATCATCTAATTGTGATTTGTATGTTTTCTCTGGTGCTGCTACATATCCAGCTTCTTCAGCTGCTTTACCTTTATCTTCTAAGACGAATTTGATAAATTCTGACATTACTTTATTATCTTTCAATGCTTTTTCATTTACATAAATGAATAATGGTCTACTTAATGCATAAGAGTTATCTTGAATTGTTTTTTTCGTAGGCTCTGTTGCTTTACCATTTTCATCTTTGATTTT  >  USA300TCH1516_ALE/1425314‑1425594

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: ‑