Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,104,016 T→C 13.4% K98K (AAA→AAG)  USA300HOU_1964 ← hypothetical bacteriophage protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,104,0160TC13.4% 64.6 / 5.5 30K98K (AAA→AAG) USA300HOU_1964hypothetical bacteriophage protein
Reads supporting (aligned to +/- strand):  ref base T (14/12);  new base C (2/2);  total (16/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.89e-01

CACTTCATGAACTTTGTACAAAATATCAATCACAATTTTTTTAACTCCCTTTTTAGCGTCTCAAAATACTTATTTTGCCCTTGTCTTATTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTGAACGTGTCCATTTTCAATTAAATGTACGATTTTATAACGGTCTTTAGAACCTCGCCAATGAACAGTAATTGTACGTTTTCCGTTTATCCATTCAGGTTTACTAAAACTTACCTCATTAATTAATGCGC  >  CP000730/2103876‑2104149
                                                                                                                                            |                                                                                                                                     
cACTTCATGAACTTTGTACAAAATATCAATCACAATTTTTTTAACTCCCTTTTTAGCGTCTCAAAATACTTATTTTGCCCTTGTCTTATTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCt                                                                                                                                       >  1:41392/1‑141 (MQ=255)
          aCTTTGTACAAAATATCAATCACAATTTTTTTAACTCCCTTTTTAGCGTCTCAAAATACTTATTTTGCCCTTGTCTTATTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTGAACgt                                                                                                                             <  1:220588/141‑1 (MQ=255)
           cTTTGTACAAAATATCAATCACAATTTTTTTAACTCCCTTTTTAGCGTCTCAAAATACTTATTTTGCCCTTGTCTTATTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTGAACgtg                                                                                                                            <  2:27269/141‑1 (MQ=255)
                  cAAAATATCAATCACAATTTTTTTAACTCCCTTTTTAGCGTCTCAAAATACTTATTTTGCCCTTGTCTTATTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTGAACGTGTCCAttt                                                                                                                     <  2:108664/141‑1 (MQ=255)
                  cAAAATATCAATCACAATTTTTTTAACTCCCTTTTTAGCGTCTCAAAATACTTATTTTGCCCTTGTCTTATTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTGAACGTGTCCAttt                                                                                                                     <  1:182063/141‑1 (MQ=255)
                   aaaaTATCAATCACAATTTTTTTAACTCCCTTTTTAGCGTCTCAAAATACTTATTTTGCCCTTGTCTTATTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTGAACGTGTCCAtttt                                                                                                                    <  1:199681/141‑1 (MQ=255)
                          caatcaCAATTTTTTTAACTCCCTTTTTAGCGTCTCAAAATACTTATTTTGCCCTTGTCTTATTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTGAACGTGTCCATTTTCAATTaa                                                                                                             >  1:70470/1‑141 (MQ=255)
                           aatcaCAATTTTTTTAACTCCCTTTTTAGCGTCTCAAAATACTTATTTTGCCCTTGTCTTATTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTGAACGTGTCCATTTTCAATTaaa                                                                                                            <  2:147168/141‑1 (MQ=255)
                                  aTTTTTTTAACTCCCTTTTTAGCGTCTCAAAATACTTATTTTGCCCTTGTCTTATTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTGAACGTGTCCATTTTCAATTAAATGTACGa                                                                                                     >  2:32451/1‑141 (MQ=255)
                                      ttttAACTCCCTTTTTAGCGTCTCAAAATACTTATTTTGCCCTTGTCTTATTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTAAATGTACCTGTTTGAACGTGTCCATTTTCAATTAAATGTACGAtttt                                                                                                 <  1:193705/141‑1 (MQ=255)
                                        ttAACTCCCTTTTTAGCGTCTCAAAATACTTATTTTGCCCTTGTCTTATTGCTCTATTAACTCCACCCAGAGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTGAACGTGTCCATTTTCAATTAAATGTACGATTTtat                                                                                               <  1:158271/141‑1 (MQ=255)
                                             tttttttttAGCGTCTCAAAATACTTATTTTGGGCTTGTCTTATTGCTCTATTAACGCCACCCATAGCTTTATTTTTTTTTATTTTTCCTGTCCCTTTTTGAACGTTTCCTTTTTCAATTAAATGTACGATTTTATAACgg                                                                                          >  2:155145/5‑141 (MQ=255)
                                             tttcTTTTTAGCGTCTCAAAATACTTATTTTGCCCTTGTCTTATTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTGAACGTGTCCATTTTCAATTAAATGTACGATTTTATAACgg                                                                                          >  2:214508/4‑141 (MQ=255)
                                             tCCCTTTTTAGCGTCTCAAAATACTTATTTTGCCCTTGTCTTATTGCTCTATTAACGCCACTCATAGCTTTATTTTTGATAAATTTACCTGTCCCTTTTTGAACGTGTCTATTTTCAATTAAATGTACGCTTGTATTACgg                                                                                          >  2:22550/1‑141 (MQ=255)
                                             tCCCTTTTTAGCGTCTCAAAATACTTATTTTGCCCTTGTCTTATTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTGAACGTGTCCATTTTCAATTAAATGTACGATTTTATAACgg                                                                                          >  1:151580/1‑141 (MQ=255)
                                                  ttttAGCGTCTCAAAATACTTATTTTGCCCTTGTCTTATTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTGAACGTGTCCATTTTCAATTAAATGTACGATTTTATAACGGTCttt                                                                                     >  1:120586/1‑141 (MQ=255)
                                                      aGCGTCTCAAAATACTTATTTTGCCCTTGTCTTATTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTTATCGTGTCTATTTTCAATTAAATGTACGATTTTATAACGGTCTTTAGaa                                                                                 >  2:81668/1‑141 (MQ=255)
                                                              aaaaTACTTATTTTGCCCTTGTCTTATTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTGAACGTGTCCATTTTCAATTAAATGTACGATTTTATAACGGTCTTTAGAACCTCGCCa                                                                         >  2:161464/1‑141 (MQ=255)
                                                                aaTACTTATTTTGCCCTTGTCTTATTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCCTTTTGAACGTGTCCATTTTCAATTAAATGTACGATTTTATAACGGTCTTTAGAACCTCGCCAAt                                                                       >  2:155543/1‑141 (MQ=255)
                                                                aaTACTTATTTTGCCCTTGTCTTATTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCCTTTTGAACGTGTCCATTTTCAATTAAATGTACGATTTTATAACGGTCTTTAGAACCTCGCCAAt                                                                       >  2:155542/1‑141 (MQ=255)
                                                                                    cTTATTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTGAACGTGTCCATTTTCAATTAAATGTACGATTTTATAACGGTCTTTAGAACCTCGCCAATGAACAGTAATTGTACGtttt                                                   <  1:247343/141‑1 (MQ=255)
                                                                                       aTTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTGAACGTGTCCATTTTCAATTAAATGTACGATTTTATAACGGTCTTTAGAACCTCGCCAATGAACAGTAATTGTACGTTTTCCg                                                >  2:10225/1‑141 (MQ=255)
                                                                                       aTTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTGAACGTGTCCATTTTCAATTAAATGTACGATTTTATAACGGTCTTTAGAACCTCGCCAATGAACAGTAATTGTACGTTTTCCg                                                >  2:138727/1‑141 (MQ=255)
                                                                                                  aaCGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTGAACGTGTCCATTTTCAATTAAATGTACGATTTTATAACGGTCTTTAGAACCTCGCCAATGAACAGTAATTGTACGTTTTCCGTTTATCCATTc                                     <  1:250240/141‑1 (MQ=255)
                                                                                                              aGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTGAACGTGTCCATTTTCAATTAAATGTACGATTTTATAACGGTCTTTAGAACCTCGCCAATGAACAGTAATTGTACGTTTTCCGTTTATCCATTCAGGTTTACTaaa                         >  2:135640/1‑141 (MQ=255)
                                                                                                                          gATAAATTTACCTGTCCCTTTTTGAACGTGTCCATTTTCAATTAAATGTACGATTTTATAACGGTCTTTAGAACCTCGCCAATGAACAGTAATTGTACGTTTTCCGTTTATCCATTCAGGTTTACTAAAACTTACCTCatt             <  1:96340/141‑1 (MQ=255)
                                                                                                                            tAAATTTACCTGTCCCCTTTTGAACGTGTCCATTTTCAATTAAATGTACGATTTTATAACGGTCTTTAGAACCTCGCCAATGAACAGTAATTGTACGTTTTCCGTTTATCCATTCAGGTTTACTAAAACTTACCTCattaa           <  1:155543/141‑1 (MQ=255)
                                                                                                                            tAAATTTACCTGTCCCCTTTTGAACGTGTCCATTTTCAATTAAATGTACGATTTTATAACGGTCTTTAGAACCTCGCCAATGAACAGTAATTGTACGTTTTCCGTTTATCCATTCAGGTTTACTAAAACTTACCTCattaa           <  1:155542/141‑1 (MQ=255)
                                                                                                                              aaTTTACCTGTCCCTTTTTGAACGTGTCCATTTTCAATTAAATGTACGATTTTATAACGGTCTTTAGAACCTCGCCAATGAACAGTAATTGTACGTTTTCCGTTTATCCATTCAGGTTTACTAAAACTTACCTCattaatt         >  1:164593/1‑141 (MQ=255)
                                                                                                                                    ccTGTCCCTTTTTGAACGTGTCCATTTTCAATTAAATGTACGATTTTATAACGGTCTTTAGAACCTCGCCAATGAACAGTAATTGTACGTTTTCCGTTTATCCATTCAGGTTTACTAAAACTTACCTCATTAATTAATgcg   >  2:213839/1‑141 (MQ=255)
                                                                                                                                     cTGTCCCTTTTTGAACGTGTCCATTTACAATTAAATGTACGATTTTATAACGGTCTTTAGAACCACGCAAAAGAACAGTAATTGTACGTTTTCCGTTTATCCATTCAGGTTTACTAAAACTTACCTCATTAATTAATgcgg  <  1:251147/141‑2 (MQ=255)
                                                                                                                                            |                                                                                                                                     
CACTTCATGAACTTTGTACAAAATATCAATCACAATTTTTTTAACTCCCTTTTTAGCGTCTCAAAATACTTATTTTGCCCTTGTCTTATTGCTCTATTAACGCCACCCATAGCTTTAGGTTTGATAAATTTACCTGTCCCTTTTTGAACGTGTCCATTTTCAATTAAATGTACGATTTTATAACGGTCTTTAGAACCTCGCCAATGAACAGTAATTGTACGTTTTCCGTTTATCCATTCAGGTTTACTAAAACTTACCTCATTAATTAATGCGC  >  CP000730/2103876‑2104149

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑