Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,934,773	T→A	6.8%	K159* (AAA→TAA)	USA300HOU_1798 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,934,773	0	T	A	6.8%	188.8 / 6.2	59	K159* (AAA→TAA)	USA300HOU_1798	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (30/25);  new base A (2/2);  total (32/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.42e-01

TCTGTCAGAAAAATATAAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCTTCTATAA  >  CP000730/1934634‑1934913                                                                                                                                            |                                                                                                                                             tCTGTCAGAAAAATATAAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATAttttt                                                                                                                                             <  2:285521/141‑1 (MQ=255)         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                                                                >  1:647091/1‑141 (MQ=255)                                                                              ttcAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTaa                                                                >  1:255484/1‑141 (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                                                   <  2:500410/141‑1 (MQ=255)                                                                                           tcCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGatat                                                   <  2:44302/141‑1 (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)                                                                                                                                            ttttGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCTTCTATaa  <  1:701372/141‑1 (MQ=255)                                                                                                                                            |                                                                                                                                             TCTGTCAGAAAAATATAAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCTTCTATAA  >  CP000730/1934634‑1934913

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: ‑