Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,338,620	G→A	8.2%	S21S (TCG→TCA)	USA300HOU_1241 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,338,620	0	G	A	8.2%	175.9 / 5.2	61	S21S (TCG→TCA)	USA300HOU_1241	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (25/31);  new base A (2/3);  total (27/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.48e-01

TTATCGATCGGTATTTTCATTTTAGTTATACTACTATTGATATTCTAAAAAATTAAAAATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGCAAAGATCTTATATGAATATGCGAAAAAGGTATTGTAATATA  >  CP000730/1338481‑1338759                                                                                                                                            |                                                                                                                                            ttATCGATCGGTATTTTCATTTTAGTTATACTACTATTGATATTCTAAAAAATTAAAAATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGa                                                                                                                                            <  2:488289/141‑1 (MQ=255)     cgatcgGTAGTTTCATTTTAGTTATACTACTATTGATATTCTAAAAAATTAAAAATTTCGCCTCAACTAATTTATGAGTAGCGAGGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTa                                                                                                                                        >  1:1083484/1‑141 (MQ=255)        tcgGTATTTTCATTTTAGTTATACTACTATTGATATTCTAAAAAATTAAAAATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCa                                                                                                                                     <  2:404752/141‑1 (MQ=255)        tcgGTATTTTCATTTTAGTTATACTACTATTGATATTCTAAAAAATTAAAAATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCa                                                                                                                                     <  1:247010/141‑1 (MQ=255)         cgGTATTTTCATTTTAGTTATACTACTATTGATATTCTAAAAAATTAAAAATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCaa                                                                                                                                    <  1:1005113/141‑1 (MQ=255)         cgGTATTTTCATTTTAGTTATACTACTATTGATATTCTAAAAAATTAAAAATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCaa                                                                                                                                    >  2:396613/1‑141 (MQ=255)           gTATTTTCATTTTAGTTATACTACTATTGATATTCTAAAAAATTAAAAATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAAt                                                                                                                                  <  2:391491/141‑1 (MQ=255)             aTTTTCATTTTAGTTATACTACTATTGATATTCTAAAAAATTAAAAATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATta                                                                                                                                >  1:746696/1‑141 (MQ=255)               tttCATTTTAGTTATACTACTATTGATATTCTAAAAAATTAAAAATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATtaat                                                                                                                              <  1:133124/141‑1 (MQ=255)                ttCATTTTAGTTATACTACTATTGATATTCTAAAAAATTAAAAATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATtaata                                                                                                                             <  1:170819/141‑1 (MQ=255)                 tCATTTTAGTTATACTACTATTGATATTCTAAAAAATTAAAAATTGCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATtaataa                                                                                                                            <  1:284767/141‑1 (MQ=255)                   aTTTTAGTTGTACTACTATTGATATTCTAAAAAATTAAAAATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATaaaa                                                                                                                          >  1:956501/1‑140 (MQ=255)                      ttAGTTATACTACTATTGATATTCTAAAAAATTAAAAATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATa                                                                                                                       <  2:663633/141‑1 (MQ=255)                         gTTATACTACTATTGATATTCTAAAAAATTAAAAATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTg                                                                                                                    <  2:874826/141‑1 (MQ=255)                            ataCTACTATTGATATTCTAAAAAATTAAACATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGa                                                                                                                 <  2:774482/141‑1 (MQ=255)                              actactATTGATATTCTAAAAAATTAAAAATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATa                                                                                                               <  2:832895/141‑1 (MQ=255)                                      tGATATTCTAAAAAATTAAAAATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACgg                                                                                                       <  1:517973/141‑1 (MQ=255)                                         tatTCTAAAAAATTAAAAATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTaa                                                                                                    >  1:418670/1‑141 (MQ=255)                                         tatTCTAAAAAATTAAAAATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTaa                                                                                                    >  1:260669/1‑141 (MQ=255)                                             cTAAAAAATTAAAAATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATAtt                                                                                                >  1:752510/1‑141 (MQ=255)                                              tAAAAAATTAAAAATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTa                                                                                               >  2:1024088/1‑141 (MQ=255)                                                 aaaattaaaaattTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAAAATTGATAGAAAACAAAGAGATATCAAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATg                                                                                            >  2:568604/1‑141 (MQ=255)                                                  aaattaaaaattTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGc                                                                                           <  2:460921/141‑1 (MQ=255)                                                             ttCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTa                                                                                <  1:423430/141‑1 (MQ=255)                                                                  cTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGagaa                                                                           >  2:980116/1‑141 (MQ=255)                                                                  cTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGagaa                                                                           <  2:397479/141‑1 (MQ=255)                                                                  cTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGagaa                                                                           >  2:612078/1‑141 (MQ=255)                                                                     aTCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAAAATTGATAGAAAACAAAGAGATATCAAGTTATCAAATTAATAAATATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTGGggaaaga                                                                        >  2:547392/1‑141 (MQ=255)                                                                        tAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAAAATTGATAGAAAACAAAGAGATATCAAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTGGGGAAagaaga                                                                     <  1:625598/141‑1 (MQ=255)                                                                            ttATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAg                                                                 <  1:879798/141‑1 (MQ=255)                                                                             tATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGAGACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGa                                                                <  2:1065514/141‑1 (MQ=255)                                                                               tGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGaaa                                                              >  2:882145/1‑141 (MQ=255)                                                                                    tGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTa                                                         >  2:428965/1‑141 (MQ=255)                                                                                       tATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGc                                                      <  1:564536/141‑1 (MQ=255)                                                                                       tATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGc                                                      <  2:580040/141‑1 (MQ=255)                                                                                       tATGATGAAATATTCAATACAATCAAAAAATTGATAGAAAACAAAGAGATATCAAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTGGGGAAAGAAGAATAGAAAATTTAAGc                                                      <  1:492352/141‑1 (MQ=255)                                                                                         tgatgaAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCtt                                                    <  2:18072/141‑1 (MQ=255)                                                                                                atatTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATCTAAGCTTAAAGAAt                                             >  1:13461/1‑141 (MQ=255)                                                                                                  atTCAATACAATCAACGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTCACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATGTAAGCTTAAAGAATGc                                           >  2:866538/1‑141 (MQ=255)                                                                                                  atTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGc                                           >  2:903549/1‑141 (MQ=255)                                                                                                  atTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGc                                           <  2:965820/141‑1 (MQ=255)                                                                                                    tCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGCaa                                         >  2:696708/1‑141 (MQ=255)                                                                                                     cAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGCaaa                                        >  2:476401/1‑141 (MQ=255)                                                                                                        tACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGCAAAGAt                                     <  1:1021219/141‑1 (MQ=255)                                                                                                        tACAATCAAAAAATTGATAGAAAACAAAGAGATATCAAGTTATCAAATTAATAAATATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTGGGGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGCAAAGAt                                     <  1:547392/141‑1 (MQ=255)                                                                                                               aaaGAATTGATAGAAAACAAAGAGATATCGTGTTATCAATTTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGCAAAGATCTTatat                              >  2:381837/1‑141 (MQ=255)                                                                                                                    aTTGATAGAAAACAAGGCGATATCGAGTTCTCAAGTTAATAAAGATACTGGGATAAGTTACGGTAATATCAAGGCTCTGCGCCGTAGAGAAAGAAGAACAGAAAACGTAAGCGTAAAGAATGCAAACATCTTATATGAata                         <  2:512548/141‑1 (MQ=255)                                                                                                                    aTTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGCAAAGATCTTATATGAata                         <  2:595754/141‑1 (MQ=255)                                                                                                                    aTTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGCAAAGATCTTATATGAata                         >  2:741532/1‑141 (MQ=255)                                                                                                                      tGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACCGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGCAGAGATCTTATATGAATATg                       >  2:246894/1‑141 (MQ=255)                                                                                                                          aGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGCAAAGATCTTATATGAATATGCGaa                   <  2:821050/141‑1 (MQ=255)                                                                                                                            aaaaCAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGCAAAGATCTTATATGAATATGCGaaaa                 >  2:1070622/1‑141 (MQ=255)                                                                                                                               aCAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGCAAAGATCTTATATGAATATGCGAAAAAgg              >  1:1047263/1‑141 (MQ=255)                                                                                                                               aCAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGCAAAGATCTTATATGAATATGCGAAAAAgg              <  1:1024088/141‑1 (MQ=255)                                                                                                                                cAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATTCAAAGATCTTATAAGAAAAAGAGAAAAAGGt             <  2:917622/141‑1 (MQ=255)                                                                                                                                   agagATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGCAAAGATCTTATATGAATATGCGAAAAAGGTAtt          >  1:1056752/1‑141 (MQ=255)                                                                                                                                   agagATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGCAAAGATCTTATATGAATATGCGAAAAAGGTAtt          >  2:784967/1‑141 (MQ=255)                                                                                                                                   agagATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTAAGGTAATATTAAAGCTATGAGACATAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGCAAAGATCTTATATGAATATGCGAAAAAGGTAtt          <  1:213035/141‑1 (MQ=255)                                                                                                                                       atatCGAGTTATCAAAATAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGCAAAGATCTTAAATGAAAAAAAAAAAAAGGTATTGTaa      <  2:331375/141‑1 (MQ=255)                                                                                                                                          tCGAGTTATCAAATTAATAAAGATACTGGGATAAGATACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGCAAAGATCTTATATGAATATGCGAAAAAGGTATTGTAatat   <  2:84622/141‑1 (MQ=255)                                                                                                                                           cGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGCAAAGATCTTATATGAATATGCGAAAAAGGTATTGTAAtata  >  1:951098/1‑141 (MQ=255)                                                                                                                                            |                                                                                                                                            TTATCGATCGGTATTTTCATTTTAGTTATACTACTATTGATATTCTAAAAAATTAAAAATTTCGCCTCATCTAATTTATGAATTGCTATGATGAAATATTCAATACAATCAAAGAATTGATAGAAAACAAAGAGATATCGAGTTATCAAATTAATAAAGATACTGGGATAAGTTACGGTAATATTAATGCTATGCGCCGTAGAGAAAGAAGAATAGAAAATTTAAGCTTAAAGAATGCAAAGATCTTATATGAATATGCGAAAAAGGTATTGTAATATA  >  CP000730/1338481‑1338759

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: ‑