Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 3,790 G→A 100% A32T (GCA→ACA)  USA300HOU_0003 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007303,7900GA93.3% 178.9 / 4.1 60A32T (GCA→ACA) USA300HOU_0003hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (1/3);  new base A (31/25);  total (32/28)
Fisher's exact test for biased strand distribution p-value = 3.31e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.86e-01
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAGCAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGCTGGTTCTTTCTTAATCAT  >  CP000730/3665‑3923
                                                                                                                             |                                                                                                                                     
tataATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTg                                                                                                                         <  2:148361/140‑1 (MQ=255)
   aataTATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCaa                                                                                                                      <  2:211449/140‑1 (MQ=255)
   aataTATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCaa                                                                                                                      <  1:74757/140‑1 (MQ=255)
    atatatTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAg                                                                                                                     <  1:115374/140‑1 (MQ=255)
        atTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGt                                                                                                                 <  2:388076/140‑1 (MQ=255)
                    cAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTGGCAAGACGTGGAGGTattaat                                                                                                     >  2:480499/1‑140 (MQ=255)
                     aaaGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTattaatt                                                                                                    >  2:667906/1‑140 (MQ=255)
                     aaaGAAATGGAGTGATTATTTTGGATCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTattaatt                                                                                                    >  1:489454/1‑140 (MQ=255)
                       aGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTAttaattaa                                                                                                  >  2:407752/1‑140 (MQ=255)
                       aGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAAAATCTAAAAACAGAAGGGAATAAAGAAACTGGAGGACAAACAAAATGGTACTAGCAAAACGTTGAAGTAtaaattaa                                                                                                  >  1:15803/1‑140 (MQ=255)
                        gAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATtaattaat                                                                                                 >  2:245299/1‑140 (MQ=255)
                        gAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGAGGTCAAACAAAATGGTTATTGCAAGACGTTGAAGTATtaattaat                                                                                                 >  2:151061/1‑140 (MQ=255)
                            tGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGATGTATTAATTAATGGAg                                                                                             <  1:377505/140‑1 (MQ=255)
                            tGGAGTGATTATTTTGGTTCAAGAAGTTGTAGAAGAAGGAGACATTCATATAGTTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAg                                                                                             >  2:731763/1‑140 (MQ=255)
                             ggAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAGCAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGt                                                                                            <  2:727477/140‑1 (MQ=255)
                                gagATTATTTAGGTACAAGAAGTTGTAGTAGAAGGAGACAATAATTTAGGTCAAATTCTAAAAACAGAAGGGAGTATTGAATCTGGTGGTAAAACAAAAAGGTTCTTGCAACCTGTTAAAGTAGTAATTAATGGAGTGCg                                                                                         >  2:690146/3‑140 (MQ=255)
                                 tGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAGCAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGt                                                                                        <  2:136134/140‑1 (MQ=255)
                                  gATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATTTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTg                                                                                       <  1:205775/140‑1 (MQ=255)
                                      attTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAac                                                                                   >  2:549329/1‑140 (MQ=255)
                                      attTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAac                                                                                   <  2:529706/140‑1 (MQ=255)
                                      attTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGAGTGaaat                                                                                   <  2:659015/140‑2 (MQ=255)
                                      attTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAAGGGAGTGCGTGAAac                                                                                   <  2:516427/140‑1 (MQ=255)
                                              taaagaagTTGTAGTAGAAGGAGACATTCATTTAGGGCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAGCAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTcgcg                                                                           <  1:359380/138‑1 (MQ=255)
                                                    agTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCGAAAAACAGAAGGGAGTATTGAATCTGGTGGTCAAGCAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTAGCGGAaaaa                                                                     >  1:178489/1‑140 (MQ=255)
                                                      ttGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAg                                                                   <  2:452472/140‑1 (MQ=255)
                                                        gtaataGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACAAGtaaagctaaaacgtt                                                                 <  2:738388/140‑15 (MQ=255)
                                                            tagAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGaa                                                             >  1:758284/1‑140 (MQ=255)
                                                            tagAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGaa                                                             >  1:483181/1‑140 (MQ=255)
                                                              gAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACa                                                           >  1:536523/1‑140 (MQ=255)
                                                              gAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAAGGGAGTGCGTGAAACACGTCGCGGTAGAAAGTTAGAACa                                                           >  2:272067/1‑140 (MQ=255)
                                                                aGGAGCCATTAATTTAGGTCAATTTTTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATc                                                         <  1:253575/140‑1 (MQ=255)
                                                                aGGAGACATTAATTTATGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAATAATTTATAACATc                                                         <  2:542997/140‑1 (MQ=255)
                                                                aGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGATGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATc                                                         <  1:10798/140‑1 (MQ=255)
                                                                aGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATc                                                         <  1:566206/140‑1 (MQ=255)
                                                                 ggAGACATTTATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCa                                                        <  2:127264/140‑1 (MQ=255)
                                                                 ggAGACAGTAATTTAGGTCAATTTCTAAAAACAGAAGGGATGATTGAAGCTGGTGGTCAAACAAAATGGTTCTTGCAAGACTTTGAAGTATTAATTAATGGAGTGCTTGAAACTCGTCGCGGTAAAAAGTTAGAACATCa                                                        <  2:380508/140‑1 (MQ=255)
                                                                   agaCATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGACAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGAAGGGCGTGAAACACGTCGCGGGAAAAAGTTAGAACATCAAg                                                      >  1:632920/1‑140 (MQ=255)
                                                                     aCATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACATGTCGCGGTAAAAAGTTAGAACATCAAGAt                                                    >  2:473896/1‑140 (MQ=255)
                                                                       aTTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCg                                                  >  2:473557/1‑140 (MQ=255)
                                                                           aTTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGCACATCAAGATCGtata                                              >  2:237028/1‑140 (MQ=255)
                                                                           aTTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGtata                                              >  1:311448/1‑140 (MQ=255)
                                                                            tttAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAg                                             <  1:667906/140‑1 (MQ=255)
                                                                                ggTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGatat                                         >  2:304028/1‑140 (MQ=255)
                                                                                    aaTTTCTAAAAGCAGAATGTATTTTTGAATTTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCa                                     <  1:480499/140‑1 (MQ=255)
                                                                                    aaTTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAAAACATCAAGATCGTATAGATATCCCa                                     >  2:683341/1‑140 (MQ=255)
                                                                                          tAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAAGGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACATCGCGGTAAAAAGTTAGAACATCACGATCGTATAGATATCCCAGAATTa                               >  2:31571/1‑140 (MQ=255)
                                                                                              aaCAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTg                           >  2:317478/1‑140 (MQ=255)
                                                                                              aaCAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAAGTACCTg                           <  2:421025/140‑1 (MQ=255)
                                                                                              aaCAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATACCAGAATTACCTg                           >  1:80543/1‑140 (MQ=255)
                                                                                                  gAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGa                       <  2:562419/140‑1 (MQ=255)
                                                                                                     gggATTATTGAATCTGGTGTTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGc                    <  1:23876/140‑1 (MQ=255)
                                                                                                     gggATTATTGAATCTGGTGGTCAAACAGAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGc                    <  1:528393/140‑1 (MQ=255)
                                                                                                      ggATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATTCCAGAATTACCTGAAGATGCt                   >  1:702126/1‑140 (MQ=255)
                                                                                                           attGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAAATGCTGGttc              >  2:612126/1‑140 (MQ=255)
                                                                                                            ttGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACATTTAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGCTGGttct             >  2:500012/1‑140 (MQ=255)
                                                                                                                    ggtggtCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGCTGGTTCTTTCTTAAt     >  1:80831/1‑140 (MQ=255)
                                                                                                                    ggtggtCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACAAGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTAACTGAAGATGCTGGTTCTTTCTTAAt     >  1:578334/1‑140 (MQ=255)
                                                                                                                     gtggtCAAACAGAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGCTGGTTCTTTCTTACtc    >  2:713874/1‑140 (MQ=255)
                                                                                                                      tggtCAAACAAAATTGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGCTGGTTCTTTCTTAAtca   <  1:52660/140‑1 (MQ=255)
                                                                                                                       ggtCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGCTGGTTCTTTCTTAAtcat  >  1:405151/1‑140 (MQ=255)
                                                                                                                             |                                                                                                                                     
TATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAGCAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGCTGGTTCTTTCTTAATCAT  >  CP000730/3665‑3923

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: