Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,119,442	T→C	7.9%	L268L (TTA→TTG)	USA300HOU_1992 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,119,442	0	T	C	7.9%	167.4 / 3.9	60	L268L (TTA→TTG)	USA300HOU_1992	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (34/21);  new base C (3/2);  total (37/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

ATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTTTGTTGTGTTTGGTTAATACGTAT  >  CP000730/2119303‑2119582                                                                                                                                            |                                                                                                                                             aTCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTa                                                                                                                                             <  2:283525/141‑1 (MQ=255)    tcGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAaat                                                                                                                                          <  2:168315/141‑1 (MQ=255)    tcGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAaat                                                                                                                                          >  1:217075/1‑141 (MQ=255)    tcGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGCAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAaat                                                                                                                                          >  2:199650/1‑141 (MQ=255)     cGTTTTAAGGTTTGCTACTGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAaatt                                                                                                                                         >  1:451228/1‑141 (MQ=255)     cGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAaatt                                                                                                                                         >  1:150850/1‑141 (MQ=255)      gTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAaatta                                                                                                                                        >  2:41402/1‑141 (MQ=255)      gTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAaatta                                                                                                                                        >  1:165682/1‑141 (MQ=255)      gTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACATAaatta                                                                                                                                        >  1:132580/1‑141 (MQ=255)           aaGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATttc                                                                                                                                   >  1:428174/1‑141 (MQ=255)             ggTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATttctt                                                                                                                                 <  1:193813/141‑1 (MQ=255)               tttGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTcc                                                                                                                               <  2:415041/141‑1 (MQ=255)                ttGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGTGCTGTTATTGTCTTCTATGCGTTTCAATTTTGATTGTTTATCAGCTAATTGATTACGCAAATTATTttctttct                                                                                                                              >  2:416462/1‑141 (MQ=255)                ttGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCt                                                                                                                              <  1:32422/141‑1 (MQ=255)                ttGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCt                                                                                                                              <  1:221029/141‑1 (MQ=255)                          tCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGTATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTg                                                                                                                    <  2:413712/141‑1 (MQ=255)                                     cgtgtagctCATTTGTTAAAGCATGTATTTTGTTCTCATTACTGGCGCTATTATTAGCTTCTATGCGCTTCAATTCTGATTGTTTATCAGCTAATTGGTTACGCAAATTAATTTCTTCTGCACCGTTTTGAATATCTATAc                                                                                                         >  1:393923/9‑141 (MQ=255)                                     cgtgtagctCATTTGTTAAAGCATGTATTTTGTTCTCATTACTGGCGCTATTATTAGCTTCTATGCGCTTCAATTCTGATTGTTTATCAGCTAATTGGTTACGCAAATTAATTTCTTCTGCACCGTTTTGAATATCTATAc                                                                                                         >  1:393940/9‑141 (MQ=255)                                     cGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATAc                                                                                                         >  2:39838/1‑141 (MQ=255)                                      gtgtAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTAAAGTTGTGGATATCTATACg                                                                                                        >  1:251078/1‑141 (MQ=255)                                        gtAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTCACGTGTTGTATATCTATACGCt                                                                                                      <  2:90742/141‑1 (MQ=255)                                        gtAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCt                                                                                                      <  1:378988/141‑1 (MQ=255)                                               aTTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTTAATATCTTTACTCTCAttttt                                                                                               >  2:413136/1‑140 (MQ=255)                                                  tGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAg                                                                                            >  1:366388/1‑141 (MQ=255)                                                       aaGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCt                                                                                       >  1:12601/1‑141 (MQ=255)                                                       aaGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCt                                                                                       <  2:72973/141‑1 (MQ=255)                                                         gCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCa                                                                                     <  2:74471/141‑1 (MQ=255)                                                                  ttGTTCTCATTACTGGCGCTATTATTAGCTTCTATGCGCTTCAATTCTGATTGTTTATCAGCTAATTGGTTACGCAAATTAATTTCTTCTGCACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGt                                                                            <  1:333051/141‑1 (MQ=255)                                                                   tGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGtt                                                                           >  2:404706/1‑141 (MQ=255)                                                                    gTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGttt                                                                          >  1:161364/1‑141 (MQ=255)                                                                     ttCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTg                                                                         >  1:328048/1‑141 (MQ=255)                                                                         cATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATaa                                                                     >  1:388936/1‑141 (MQ=255)                                                                             aCTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGc                                                                 >  1:334456/1‑141 (MQ=255)                                                                                   gcTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGtatct                                                           >  2:367865/1‑141 (MQ=255)                                                                                       ttATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCa                                                       >  2:431108/1‑141 (MQ=255)                                                                                        tATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCAt                                                      >  2:190090/1‑141 (MQ=255)                                                                                           tGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTAt                                                   <  1:59772/141‑1 (MQ=255)                                                                                           tGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTAt                                                   <  1:230739/141‑1 (MQ=255)                                                                                            gTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATc                                                  >  1:204850/1‑141 (MQ=255)                                                                                                 ctATGCGTTTCAATTCTGATTGTTTATCAACTAATTGGTTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACACTCATTTTCATGTTGCGCAATTTCTTGTTTGATAATTTAGTAGCTATCGTTATCGTAtt                                             >  2:107066/1‑141 (MQ=255)                                                                                                  tATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTc                                            >  1:389059/1‑141 (MQ=255)                                                                                                  tATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTc                                            >  2:58130/1‑141 (MQ=255)                                                                                                        tttCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTAc                                      >  1:15831/1‑141 (MQ=255)                                                                                                        cttCCATTCTGATTGTTTATCAGCTCATTGGTTACGCAAATTATTTTCTTCCGCACCCATCTGAATATCTATACGCTAACTTTCTCGTTGCTCAATTTCTTGTTTTATGATTGTGTGTCTATCATTATCGAATTCCGGTAc                                      <  1:269986/140‑1 (MQ=255)                                                                                                           cAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATc                                   >  2:199908/1‑141 (MQ=255)                                                                                                           cAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATc                                   <  1:321196/141‑1 (MQ=255)                                                                                                           cAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATc                                   >  1:48436/1‑141 (MQ=255)                                                                                                           cAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTCCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATc                                   <  1:372627/141‑1 (MQ=255)                                                                                                                cTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCt                              <  2:117313/141‑1 (MQ=255)                                                                                                                 tGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCtt                             <  1:453720/141‑1 (MQ=255)                                                                                                                  taTTGTTTATCAGCTAATTGATTTCGTAAATTATTTTCTTTCTTACTTTTTTGAATATCTATACGGTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCTTTATCGAATTCTGTTACATCCTGCTTa                            <  2:333773/140‑1 (MQ=255)                                                                                                                   aTTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTTCCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTAt                           <  1:221610/141‑1 (MQ=255)                                                                                                                     tGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTAttt                         <  1:274684/141‑1 (MQ=255)                                                                                                                      gTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCACTTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTAtttt                        >  1:233748/1‑141 (MQ=255)                                                                                                                      gTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTAtttt                        >  2:383532/1‑141 (MQ=255)                                                                                                                         tATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTttgtt                     >  2:220968/1‑141 (MQ=255)                                                                                                                          aTCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTttgttg                    >  1:174948/1‑141 (MQ=255)                                                                                                                             aGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTTTGTTgtgt                 <  1:348084/141‑1 (MQ=255)                                                                                                                                  aTTGATTACGTAAATTAATTTCTTCCTTACTGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCATGCTTATTTTGTTGTGTTTGGt            >  1:255567/1‑141 (MQ=255)                                                                                                                                         aCGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTTTGTTGTGTTTGGTTAATACg     >  2:168201/1‑141 (MQ=255)                                                                                                                                            tAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTTTGTTGTGTTTGGTTAATACGTAt  >  2:450912/1‑141 (MQ=255)                                                                                                                                            |                                                                                                                                             ATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTTTGTTGTGTTTGGTTAATACGTAT  >  CP000730/2119303‑2119582

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