Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,386,119	G→A	62.5%	P114L (CCG→CTG)	USA300HOU_2245 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,386,119	0	G	A	62.5%	35.2 / 55.3	61	P114L (CCG→CTG)	USA300HOU_2245	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (13/9);  new base A (17/20);  total (30/31)
Fisher's exact test for biased strand distribution p-value = 4.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.30e-01

TTTTTAGTACGCATGGAATCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGACTCC  >  CP000730/2385981‑2386249                                                                                                                                           |                                                                                                                                   tttttAGTACGCATGGAATCACTTTCTTCCCATTGGATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCgg                                                                                                                                   <  1:515444/140‑1 (MQ=255)         aCGCATGGAATCACTTTCTTCCAATTTAATTAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCctacta                                                                                                                           <  2:149623/140‑1 (MQ=255)            cATGGAATCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACtt                                                                                                                        <  1:603669/140‑1 (MQ=255)              tGGAATCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCa                                                                                                                      >  2:721711/1‑140 (MQ=255)               ggAATCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCaa                                                                                                                     <  1:698527/140‑1 (MQ=255)                 aaTCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAAcc                                                                                                                   >  1:196856/1‑140 (MQ=255)                  aTCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCt                                                                                                                  <  1:110167/140‑1 (MQ=255)                   tCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTg                                                                                                                 >  1:59883/1‑140 (MQ=255)                              ccATTGAATAAACAATGGTTGCGTCATTTCATCATCATCCTGATTCATTATATAAAGCAATCGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTa                                                                                                      <  1:14272/140‑1 (MQ=255)                              ccATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTa                                                                                                      <  1:207271/140‑1 (MQ=255)                               cATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAg                                                                                                     >  1:34676/1‑140 (MQ=255)                                 ttGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATTTAAAGCAATTGCCATTTTACCTTACCATTTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGtt                                                                                                   <  1:265136/140‑1 (MQ=255)                                 ttGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGtt                                                                                                   <  2:532890/140‑1 (MQ=255)                                 ttGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGtt                                                                                                   <  1:362782/140‑1 (MQ=255)                                  tGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATCAATTATATAAAGAAATTGCCACTTTACCTTACCATCTTTATGTGTATCGCTTTCCCATTGACTCGGCCCTACTACTTCAACCTGCTCACCATGTAGttt                                                                                                  >  2:312413/1‑140 (MQ=255)                                   gAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTa                                                                                                 >  2:539296/1‑140 (MQ=255)                                       aaaaaaTGTCGCCTTACTTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATCTGTACCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTAtttt                                                                                             <  1:591305/140‑1 (MQ=255)                                       aaaaaaTGGTGGCTTAATTTCATCATCATCCTTATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCCTTTTAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTAtttt                                                                                             <  2:119347/140‑1 (MQ=255)                                       aaaaaaTGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTAtttt                                                                                             <  1:668806/140‑1 (MQ=255)                                       aaaaaaTGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTAtttt                                                                                             <  2:544035/140‑1 (MQ=255)                                        aaaaaTGGTGGCTTAATTTCATCATCCTCCTTGTTCATTATATAAAGCACTTGCCACTTTACCTTACCCTCTTTATGTGTAGCTCTTTCCATTTGAATCTTCCCTACTACTTCCAGCTGGTCACTTTTTAGTTTAttttt                                                                                            <  2:397782/140‑1 (MQ=255)                                        aaaaaTGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTAttttt                                                                                            <  2:656568/140‑1 (MQ=255)                                        aaaaaTGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTAttttt                                                                                            <  1:229955/140‑1 (MQ=255)                                            aTGGTGGCTTAATTTCCTCATGATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACt                                                                                        >  1:372401/1‑140 (MQ=255)                                                tggCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGACCTACTACTTCAAGCTGCTCACTTTGTAGTTTATATTTGACTACct                                                                                    >  1:494047/1‑140 (MQ=255)                                                   cTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCCCTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCGCTTTGTAGTTTATTTTTTACTGCCTCta                                                                                 >  2:63955/1‑140 (MQ=255)                                                           catcatcatCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCAttt                                                                         <  1:651971/140‑1 (MQ=255)                                                           catcatcatCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCAttt                                                                         <  2:196856/140‑1 (MQ=255)                                                             tcatcatcCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCATCTATATAATTTGt                                                                       >  1:323319/1‑140 (MQ=255)                                                                 catcCTGATTCATTATATAAAGCAATTGCCACTTTATATGACCATCTTTATGTGGAGCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGc                                                                   >  1:716959/1‑140 (MQ=255)                                                                    ccTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTTAATCAGCCCTACTACTTCAACCTACTCACTTTGTAGTTTCTTTTTAACTGCCTCTATATCCTTTTTACGccaa                                                                >  2:659738/1‑140 (MQ=255)                                                                      tGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTGGTACGcaaaca                                                              >  1:693217/1‑140 (MQ=255)                                                                             ttATTTAAAGCAATTGCCACTTTACCTTAGCGTCTTTATGTGTATCTTTTTCCATTTGAATCAGTCCTACTACTTCAACATGCTCACTTTGTAGTTTATTTTTAACTGACTCTACATCATTTGTACGCAAACAAATAttt                                                       <  2:347523/140‑1 (MQ=255)                                                                             ttATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATAttt                                                       >  1:623796/1‑140 (MQ=255)                                                                             ttATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATAttt                                                       >  1:246115/1‑140 (MQ=255)                                                                               atataAAGCAATTGCGACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATAttttt                                                     >  1:541300/1‑140 (MQ=255)                                                                               atataAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATAttttt                                                     <  1:50884/140‑1 (MQ=255)                                                                                 ataAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTaa                                                   <  1:117524/140‑1 (MQ=255)                                                                                    aaGCAATTTCCCCTTTACCTTACCATCTTTATGTGTATCTCTTTTCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGc                                                <  1:61353/140‑1 (MQ=255)                                                                                          ttGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCt                                          >  1:124010/1‑140 (MQ=255)                                                                                           tGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTc                                         <  1:54910/140‑1 (MQ=255)                                                                                             ccACTTTTCCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCAt                                       <  2:176066/140‑1 (MQ=255)                                                                                             ccACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTTTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCAt                                       >  1:67947/1‑140 (MQ=255)                                                                                             ccACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATAATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCAt                                       >  1:668229/1‑140 (MQ=255)                                                                                             ccACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCAt                                       <  2:681577/140‑1 (MQ=255)                                                                                               aCTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCCTTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATAc                                     >  1:97754/1‑140 (MQ=255)                                                                                               aCTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATAc                                     >  1:312177/1‑140 (MQ=255)                                                                                                cTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACt                                    >  2:574855/1‑140 (MQ=255)                                                                                                     ccttaccATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTctct                               >  2:517515/1‑140 (MQ=255)                                                                                                     ccttaccATCTTTATGTGTATCTCTTTCCATTTGAAGCAGCCCTACTACATCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTctct                               >  2:81985/1‑140 (MQ=255)                                                                                                      cttaccATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCtt                              >  1:219288/1‑140 (MQ=255)                                                                                                             tCTGTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGATCACTTCGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATCTTTAAAGCCTTGCTCATACTTCTCTTGAACAAt                       <  2:479895/140‑1 (MQ=255)                                                                                                                     tgtCTCTCTTTCCCTTTGAATCACACCTTCTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCTTTTATATCATTTGTACGCAAACAAATATTTTTAAAGCATTTGCAGTAGTTCTCTTGAACAATTTGAGTAg               <  2:155192/140‑1 (MQ=255)                                                                                                                      gtATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTTCTCATTTTGTATTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGc              <  1:558719/140‑1 (MQ=255)                                                                                                                       tATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTCTTTTTAACTGCCTCTATATCATTTGTACGCCAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGGAGCa             >  2:453983/1‑140 (MQ=255)                                                                                                                           tctTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAg         <  2:34676/140‑1 (MQ=255)                                                                                                                            ctTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAACGCCTTGCTCATACTTCTCTTGAACAATTTGCGTCGCACAAGc        >  2:284309/1‑140 (MQ=255)                                                                                                                            ctTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGc        >  1:484649/1‑140 (MQ=255)                                                                                                                            ctTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGATCATACTTCTCTTTAACAATTTGAGTAGCAAAAgt        >  1:126993/1‑139 (MQ=255)                                                                                                                               tCCATTTGCATCTGCCCCACTACTTCAACCTTCTTACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAATAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGAc     <  1:37112/140‑1 (MQ=255)                                                                                                                               tCCATTTGAATCGGCCCTACTTCTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGAc     <  2:586557/140‑1 (MQ=255)                                                                                                                                  aTTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGATTcc  >  1:522331/1‑140 (MQ=255)                                                                                                                                           |                                                                                                                                   TTTTTAGTACGCATGGAATCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGACTCC  >  CP000730/2385981‑2386249

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑