Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,419,5270GT21.1% 120.2 / 23.9 52P7T (CCT→ACT) USA300HOU_RS07040hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (22/19);  new base T (5/6);  total (27/25)
Fisher's exact test for biased strand distribution p-value = 7.40e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.12e-01
Rejected as consensus: Frequency below/above cutoff threshold.

GAAAATTTGGAATAAAAAATGCAAGCACACCTAATATAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATTCTATCTACTAATAGAAAAATCATTGTT  >  USA300TCH1516_ALE/1419389‑1419666
                                                                                                                                          |                                                                                                                                           
gAAAATTTGGAATAAAAAATGCAAGCACACCTAATATAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCa                                                                                                                                           >  1:460711/1‑141 (MQ=255)
    aTTTGGAATAAAAAATGCAAGCACACCTAATATAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATc                                                                                                                                       <  1:876258/141‑1 (MQ=255)
     tttGGAATAAAAAATGCAAGCACACCTAATATAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCg                                                                                                                                      <  2:353854/141‑1 (MQ=255)
       tGGAATAAAAAATGCAAGCACACCTAATATAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGaa                                                                                                                                    >  1:421495/1‑141 (MQ=255)
            tAAAAAATGCAAGCACACCTAATATAACAAATGTAATTACTGCAGATACAAACCGTTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATg                                                                                                                               <  1:310475/141‑1 (MQ=255)
                aaaTGCAAGCACACCTAATATAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCat                                                                                                                           >  1:343442/1‑141 (MQ=255)
                    gCAAGCACACCTAATATAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATattc                                                                                                                       >  1:468564/1‑141 (MQ=255)
                    gCAAGCACACCTAATATAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATattc                                                                                                                       <  2:387933/141‑1 (MQ=255)
                     cAAGCACACCTAATATAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATattca                                                                                                                      >  1:111813/1‑141 (MQ=255)
                          acacCTAATATAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATtctc                                                                                                                 <  1:507154/141‑1 (MQ=255)
                            acCTAATATAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCt                                                                                                               >  2:140268/1‑141 (MQ=255)
                                     aaCAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTTAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCa                                                                                                      <  1:773834/141‑1 (MQ=255)
                                        aaaTGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTa                                                                                                   >  1:110210/1‑141 (MQ=255)
                                                   cTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGta                                                                                        <  2:401386/141‑1 (MQ=255)
                                                        gATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACAt                                                                                   >  2:264751/1‑141 (MQ=255)
                                                               aCCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTttatta                                                                            >  1:281037/1‑141 (MQ=255)
                                                               aCCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTttatta                                                                            >  1:953798/1‑141 (MQ=255)
                                                                    ttatttaAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAAt                                                                       <  1:741237/141‑1 (MQ=255)
                                                                     tatttaAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTCTACATTTTATTATAAAtt                                                                      <  2:417812/141‑1 (MQ=255)
                                                                     tatttaAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAAtt                                                                      >  1:463534/1‑141 (MQ=255)
                                                                      atttaAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAAttt                                                                     >  2:76035/1‑141 (MQ=255)
                                                                        ttaAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATCTTCATTCTCCTTTTATTTCATTACTTTTCTTGTATACATTTTGTTATAAAttttt                                                                   >  1:778845/1‑141 (MQ=255)
                                                                               tAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACt                                                            <  1:682555/141‑1 (MQ=255)
                                                                               aaaGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACt                                                            <  2:162038/140‑1 (MQ=255)
                                                                                 aGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCTTATAATGTCATTTTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTa                                                          >  1:638179/1‑141 (MQ=255)
                                                                                  gCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTaa                                                         >  2:413381/1‑141 (MQ=255)
                                                                                   cAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTaaa                                                        >  1:145279/1‑141 (MQ=255)
                                                                                     aCAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATAGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACa                                                      >  1:315659/1‑141 (MQ=255)
                                                                                        gAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATa                                                   >  1:852148/1‑141 (MQ=255)
                                                                                                 taataaAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGcagtcagt                                          <  2:98298/141‑1 (MQ=255)
                                                                                                  aataaAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGtt                                         <  1:356709/141‑1 (MQ=255)
                                                                                                  aataaAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGtt                                         >  1:96539/1‑141 (MQ=255)
                                                                                                    taaATTCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTc                                       >  1:961252/1‑141 (MQ=255)
                                                                                                     aaaaTCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTCTTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCa                                      <  1:718862/141‑1 (MQ=255)
                                                                                                         tCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCa                                  >  2:375418/1‑141 (MQ=255)
                                                                                                          cATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCaa                                 <  1:205728/141‑1 (MQ=255)
                                                                                                           attattAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAat                                >  1:448378/1‑141 (MQ=255)
                                                                                                            ttattaATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAata                               <  2:238262/141‑1 (MQ=255)
                                                                                                             tattaATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAatat                              >  1:707653/1‑141 (MQ=255)
                                                                                                                taATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATtct                           <  1:932280/141‑1 (MQ=255)
                                                                                                                taATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATtct                           <  2:8082/141‑1 (MQ=255)
                                                                                                                  aTGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATtctat                         <  1:158497/141‑1 (MQ=255)
                                                                                                                  aTGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATtctat                         <  1:561958/141‑1 (MQ=255)
                                                                                                                    gttgtGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATtctatct                       <  1:62229/141‑1 (MQ=255)
                                                                                                                       gtgATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATTCTATctact                    <  1:261967/141‑1 (MQ=255)
                                                                                                                          aTCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATTCTATCTACTAAt                 >  2:328051/1‑141 (MQ=255)
                                                                                                                           tCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATTCTATCTACTAATa                <  1:417280/141‑1 (MQ=255)
                                                                                                                                 aataatTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATTCTATCTACTAATAGaaaaa          >  1:663288/1‑141 (MQ=255)
                                                                                                                                 aataatTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATTCTATCTACTAATAGaaaaa          <  1:804025/141‑1 (MQ=255)
                                                                                                                                       tAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATTCTATCTACTAATAGAAAAATCATTg    >  1:495329/1‑141 (MQ=255)
                                                                                                                                        aGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATTCTATCTACTAATAGAAAAATCATTGt   <  1:668231/141‑1 (MQ=255)
                                                                                                                                        aGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATTCTATCTACTAATAGAAAAATCATTGt   >  1:854459/1‑141 (MQ=255)
                                                                                                                                         ggCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATTCTATCTACTAATAGAAAAATCATTGtt  >  1:717716/1‑141 (MQ=255)
                                                                                                                                          |                                                                                                                                           
GAAAATTTGGAATAAAAAATGCAAGCACACCTAATATAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATTCTATCTACTAATAGAAAAATCATTGTT  >  USA300TCH1516_ALE/1419389‑1419666

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑