Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 584,121 G→T 100% intergenic (+205/‑67) rplA → / → rplJ 50S ribosomal protein L1/50S ribosomal protein L10

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE584,1210GT98.4% 109.3 / ‑6.3 38intergenic (+205/‑67)rplA/rplJ50S ribosomal protein L1/50S ribosomal protein L10
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base T (24/12);  minor base C (2/0);  total (26/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TAATTTCCAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCGTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCAAAT  >  USA300TCH1516_ALE/583985‑584250
                                                                                                                                        |                                                                                                                                 
tAATTTCCAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTggg                                                                                                                               >  1:123160/1‑141 (MQ=255)
  aTTTCCAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTa                                                                                                                             >  2:332759/1‑141 (MQ=255)
                ttACTTATTGTAATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTTACCTGCCGAGGCTAAAATTAACTTGAAAGTGATGATCTATAACCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCtttttt                                                                                                               >  2:105570/1‑141 (MQ=255)
                           gATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTa                                                                                                    >  2:323601/1‑141 (MQ=255)
                               attTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAGGTGCTTTTTTTATTAATTTTaaaaa                                                                                                >  2:277716/1‑141 (MQ=255)
                                  ttACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAg                                                                                             >  1:295734/1‑141 (MQ=255)
                                   tACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGc                                                                                            >  1:129408/1‑141 (MQ=255)
                                    acgtAAGACAGTCGGAGTTATTTATAACTTAAAATTTATCCTGCCGGGGCGAAAATTGACTTGAACGTGATGATCTAGGAGCTTTCAAGCACTTTCTGACTTTGGCAGTAAGTGTTTTTTTTATTATTTTTaaaacaatcc                                                                                           >  2:331496/4‑138 (MQ=255)
                                    aCCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCa                                                                                           >  1:145832/1‑141 (MQ=255)
                                     ccTAAGACAGTAGGAGGTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGACCGTGATGGTCTATGATCTTTCAAACACTTTTTGCCTTGGGTAGAACGTGCTTGTTTTATTAATTTTATAAAAAGCAc                                                                                          >  1:46802/1‑141 (MQ=255)
                                        aaGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCaa                                                                                       <  2:150362/141‑1 (MQ=255)
                                                 ggAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAAtt                                                                                  >  2:329614/1‑137 (MQ=255)
                                                 ggAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAAtt                                                                                  <  1:329614/137‑1 (MQ=255)
                                                  gAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAAt                                                                             >  2:218730/1‑141 (MQ=255)
                                                  gAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAAt                                                                             >  1:297565/1‑141 (MQ=255)
                                                  gAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAAt                                                                             >  1:103662/1‑141 (MQ=255)
                                                    gTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCCTGGGTACAACTTGCGTGTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATgg                                                                           >  1:204053/1‑141 (MQ=255)
                                                    gTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTGTTGCCTTGGGTAGAAAGTGCTTTTTTTAATAATTTTAAATGAAGCACCAAAACTTTAAATga                                                                           >  2:336759/1‑140 (MQ=255)
                                                      tatttatAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAg                                                                         <  2:51756/141‑1 (MQ=255)
                                                          tataACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGACTTGGGTAGAAAGTGCTTTTTTTATTAATTTTATAAAAAGCACCAAAAATTTAAATGAAGgtgt                                                                     >  2:125047/1‑141 (MQ=255)
                                                                  aaaaTTTATCCTGCCGGGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGt                                                             <  1:169645/141‑1 (MQ=255)
                                                                      tttATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGCGGTGTCTGAATGTCTGc                                                         >  1:45091/1‑141 (MQ=255)
                                                                      tttATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGc                                                         <  1:331107/141‑1 (MQ=255)
                                                                      tttATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAAGGGAGGTGTCTGGATGTCTGc                                                         >  2:142182/1‑141 (MQ=255)
                                                                            cTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCAt                                                   >  2:121845/1‑141 (MQ=255)
                                                                                cGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGaa                                               >  1:122220/1‑141 (MQ=255)
                                                                                  gggCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGc                                             <  1:274314/140‑1 (MQ=255)
                                                                                    gCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTa                                           >  1:26626/1‑141 (MQ=255)
                                                                                             gACTCGCACGTGAGCACCTATGGCCTTTCATGCACTTTTGGCATTGGGTAGAATGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAaacaac                                  <  2:188583/141‑1 (MQ=255)
                                                                                                 tGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAACAAACAACTAGt                              >  2:16610/1‑141 (MQ=255)
                                                                                                     cGTGATGATCCATGCTCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTtgat                          <  1:313329/141‑1 (MQ=255)
                                                                                                            atctatgatctTTCAAGCACATTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTg                   <  1:279592/141‑1 (MQ=255)
                                                                                                             tctaggatctTTCAAGCACTTTTTGACCTGGGAAGCAAGTGCTTTTTTTTTCAATTTTAAAAAAAGCACCAAAAATTTAAATGGATGAATGCAAGTATCTCATATCAATCAAGCTAAAAAACAACTAGTTGATTAAAttac                  >  2:142931/1‑139 (MQ=255)
                                                                                                                 tgatctTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAATCAACTAGTTGATGAAATTGCTGAg              <  1:227890/141‑1 (MQ=255)
                                                                                                                         cAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTAATGAAATTGCTGAGGTACTATc      >  1:79590/1‑141 (MQ=255)
                                                                                                                           aGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATGTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCaa    >  1:69447/1‑141 (MQ=255)
                                                                                                                             cACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCAAAt  <  1:131233/141‑1 (MQ=255)
                                                                                                                             cACTTTTTGCCTTGGGTAGAAAGTCCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCAAAt  <  1:182796/141‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                 
TAATTTCCAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCGTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCAAAT  >  USA300TCH1516_ALE/583985‑584250

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑