Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,119,394	G→A	7.4%	D284D (GAC→GAT) ‡	USA300HOU_1992 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,119,394	0	G	A	7.4%	153.2 / 2.7	54	D284D (GAC→GAT) ‡	USA300HOU_1992	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (28/22);  new base A (2/2);  total (30/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.59e-01

TACGTCTATTTTCTTCATGCGTGATTTGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATC  >  CP000730/2119258‑2119534                                                                                                                                         |                                                                                                                                             tACGTCTATTTTCTTCATGCGTGATTTGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGtctt                                                                                                                                          >  1:163572/1‑141 (MQ=255)        aTTTTCTTCATGCGTGATTTGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCg                                                                                                                                   <  2:429852/141‑1 (MQ=255)        aTTTTCTTCATGCGTGATTTGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCg                                                                                                                                   <  2:59169/141‑1 (MQ=255)               tcATGCGTGATTTGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAAt                                                                                                                            >  1:454619/1‑141 (MQ=255)                cATGCGTGATTTGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAAtt                                                                                                                           <  2:432227/141‑1 (MQ=255)                    cGTGATTTGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGa                                                                                                                       <  1:58910/141‑1 (MQ=255)                    cGTGATTTGTTGTTAGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGACTTCTATACGTTTCAATTCTgt                                                                                                                       >  2:431024/1‑140 (MQ=255)                       gATTTGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTg                                                                                                                    <  1:400361/141‑1 (MQ=255)                        aTTTGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGt                                                                                                                   <  2:92287/141‑1 (MQ=255)                         tttGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGtt                                                                                                                  >  1:137618/1‑141 (MQ=255)                         tttGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGtt                                                                                                                  >  1:137635/1‑141 (MQ=255)                               gtttgtttTGCTTTAATCTTGTTTTAAGATTCGCAACCGTTCCATTTTCAACGTGTAGCTCATTTGTTAAAGCATGTATTTTGTTCTCATTACTGGCGCTATTATTAGCTTCTATGCGCTTCAATTCTGATTGTTTATCAg                                                                                                            <  2:290880/141‑1 (MQ=255)                                 ttgtttTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTTTTTTGTTAAAGCATGGCTTTTGTTCTCATTGCTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGCTTGTTTATCAGCt                                                                                                          <  2:75748/141‑1 (MQ=255)                                  tgtttTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTa                                                                                                         <  1:158869/141‑1 (MQ=255)                                         cTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGAtt                                                                                                  >  1:326868/1‑141 (MQ=255)                                            tAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACg                                                                                               <  1:240729/141‑1 (MQ=255)                                              aTCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTa                                                                                             <  2:283525/141‑1 (MQ=255)                                                 tcGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAaat                                                                                          >  1:217075/1‑141 (MQ=255)                                                 tcGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAaat                                                                                          <  2:168315/141‑1 (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)                                                                                                                                         |                                                                                                                                             TACGTCTATTTTCTTCATGCGTGATTTGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATC  >  CP000730/2119258‑2119534

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑