Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,934,780	A→T	14.3%	N156K (AAT→AAA)	USA300HOU_1798 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,934,780	0	A	T	14.3%	158.7 / 11.7	63	N156K (AAT→AAA)	USA300HOU_1798	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (26/27);  new base T (8/2);  total (34/29)
Fisher's exact test for biased strand distribution p-value = 9.23e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAAAATATAAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCTTCTATAATTTT  >  CP000730/1934642‑1934917                                                                                                                                           |                                                                                                                                          aaaaaTATAAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTTAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTTTTCTAAATTAGAGAATATTTTTTTGAAAtt                                                                                                                                         >  2:701372/1‑141 (MQ=255) aaaaaTATAAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAAtt                                                                                                                                         >  1:94072/1‑141 (MQ=255)  aaaaTATAAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTc                                                                                                                                        >  1:138436/1‑141 (MQ=255)    aaTATAAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGTAATTTaa                                                                                                                                      >  1:537015/1‑141 (MQ=255)      tataAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCaaat                                                                                                                                    >  2:108003/1‑141 (MQ=255)       ataAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTATTTGAATTTCaaaaa                                                                                                                                   <  1:56921/141‑3 (MQ=255)        taAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGTCTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCaaataa                                                                                                                                  >  2:23729/1‑141 (MQ=255)        taAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCaaataa                                                                                                                                  <  2:345551/141‑1 (MQ=255)          aGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCaaataaat                                                                                                                                <  1:105477/141‑1 (MQ=255)              tCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTATTTGAATTTCAAAAAAATATTc                                                                                                                            <  1:435949/141‑1 (MQ=255)                 atatTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAAGATTCttt                                                                                                                         <  1:509493/141‑1 (MQ=255)                    ttAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCg                                                                                                                      <  1:258284/141‑1 (MQ=255)                    ttAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCg                                                                                                                      <  2:701821/141‑1 (MQ=255)                       aTTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTAt                                                                                                                   <  2:13410/141‑1 (MQ=255)                            atCTATCAATACATAGAATTCCCTTAAGTATTTTATCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGa                                                                                                              <  2:353764/140‑1 (MQ=255)                               tATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGAttt                                                                                                           <  2:67873/141‑1 (MQ=255)                                      tCATAAATTTCACTTAAGTATTTTTTTTTTTTTTTTAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAATTTCAAATAAATATTCTTTGAGTATTTTTATTTcttcttt                                                                                                    >  2:641490/1‑140 (MQ=255)                                      tCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCATACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAAAGAATATTTTTTTGAAATTCAAATATATATTTTTTGCGTATTTTGATTTCATCttt                                                                                                    >  1:350873/1‑140 (MQ=255)                                        aTAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATc                                                                                                  <  1:256251/141‑1 (MQ=255)                                             tttCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTaaaa                                                                                             >  1:204601/1‑141 (MQ=255)                                              ttCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAat                                                                                            <  2:662942/141‑1 (MQ=255)                                                  cTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCa                                                                                        >  1:329169/1‑141 (MQ=255)                                                  cTTAAGTATTTTTTCTTTTCTTCAAACTATTCTTCCAGTTCCAAATAATTATTGATTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTTAAATAAATATTGTTAGCGTATTTTGATTTAATCTTATCTAAAatataa                                                                                        >  2:733358/1‑139 (MQ=255)                                                     aaGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCAttt                                                                                     <  1:776684/141‑1 (MQ=255)                                                      aGTATTTTTTCTTTTCTTTAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCTAATAAATATTCTTTGCTTTTTTTGATTTCATCTTATCTAAAATATCAtttt                                                                                    >  2:535601/1‑141 (MQ=255)                                                      aGTATTTTTTCTTTTCTTCAAACTCTTCATCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCAtttt                                                                                    <  1:86989/141‑1 (MQ=255)                                                       gTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTc                                                                                   <  1:240076/141‑1 (MQ=255)                                                            ttttcttttcTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGatat                                                                              <  2:134844/141‑1 (MQ=255)                                                                   tttttttaaCTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTTTTTTTTTTTTTTTTTTCGTATTTTGATTTCATCTTATCTAAAATATCTTTTTCGATATAACCttt                                                                       >  2:752069/8‑141 (MQ=255)                                                                   ttcttcAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCttt                                                                       <  2:636326/141‑1 (MQ=255)                                                                    tcttcAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAGATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCtttt                                                                      <  1:197868/141‑1 (MQ=255)                                                                     cttcAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTa                                                                     >  1:226781/1‑141 (MQ=255)                                                                     cttcAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTa                                                                     <  2:611079/141‑1 (MQ=255)                                                                      ttcAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTaa                                                                    >  1:255484/1‑141 (MQ=255)                                                                      ttcAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTaa                                                                    >  1:647091/1‑141 (MQ=255)                                                                         aaaCTCTTCTTTCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTc                                                                 <  1:38313/141‑1 (MQ=255)                                                                              cttcttCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTa                                                            >  2:317586/1‑141 (MQ=255)                                                                               ttcttcCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAg                                                           >  1:501204/1‑141 (MQ=255)                                                                                tcttcCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGa                                                          >  2:644809/1‑141 (MQ=255)                                                                                   tcCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGatat                                                       <  2:44302/141‑1 (MQ=255)                                                                                   tcCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGatat                                                       <  2:500410/141‑1 (MQ=255)                                                                                        ttCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAat                                                  >  1:229304/1‑141 (MQ=255)                                                                                        ttCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTCTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAat                                                  <  1:619543/141‑1 (MQ=255)                                                                                          ccAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAatat                                                >  2:207976/1‑141 (MQ=255)                                                                                                 attattGACTGATTGTTCTAAATTAGAGAATATTTTTTTTTTTTTTTTTTAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATTAAATATTAGtatt                                         >  2:382014/1‑140 (MQ=255)                                                                                                   tattGACTAATTGTACTAACTTAGATAATATTTTTTTTAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCTATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATAtt                                       <  2:783473/141‑1 (MQ=255)                                                                                                    attGACTGATTGTTCTAAATTAGAGAATATTTTTTTTTTTTTTTTTTAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATAttt                                      >  2:508730/1‑141 (MQ=255)                                                                                                     ttGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTa                                     >  2:114841/1‑141 (MQ=255)                                                                                                     ttGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTa                                     >  1:57177/1‑141 (MQ=255)                                                                                                              tGTTCTAAATTAGAGAATATTTTTTTTTTTTTCAATTAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAattattt                            >  2:499678/1‑140 (MQ=255)                                                                                                                ttCTAAATTAGAGAATATTTTTTTTTTTTTTATATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGt                          >  2:409199/1‑141 (MQ=255)                                                                                                                 tCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTa                         >  1:56997/1‑141 (MQ=255)                                                                                                                  cTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTaa                        <  1:357820/141‑1 (MQ=255)                                                                                                                     aaTTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAg                     >  2:743650/1‑141 (MQ=255)                                                                                                                         agagAATATTTTTTTTAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAAt                 >  2:332387/1‑141 (MQ=255)                                                                                                                         agagAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAAt                 <  2:520787/141‑1 (MQ=255)                                                                                                                           tgaATATTTTTTTTAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAGCCTTTTAATTCTGTTAGATATTAAATATTAGTATATTTAAAATTATTGGTAATAGAAATAc               <  2:662166/140‑1 (MQ=255)                                                                                                                           agaATATTTATTTGAATTTCAAAAAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTTGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATAc               >  2:227357/1‑141 (MQ=255)                                                                                                                             aaTATTTATTTGAATTTCAAAAAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCt             >  1:447935/1‑141 (MQ=255)                                                                                                                                  ttatttGAATTTCAAAAAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCTTCtat        >  1:398683/4‑141 (MQ=255)                                                                                                                                    ttttGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCTTCTATaa      <  1:701372/141‑1 (MQ=255)                                                                                                                                        gAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCTTCTATAAtttt  >  1:388699/1‑141 (MQ=255)                                                                                                                                        gAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCTTCTATAAtttt  <  1:4882/141‑1 (MQ=255)                                                                                                                                           |                                                                                                                                          AAAAATATAAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCTTCTATAATTTT  >  CP000730/1934642‑1934917

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: ‑