Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	160,585	A→G	7.0%	M260V (ATG→GTG)	deoB →	Phosphopentomutase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	160,585	0	A	G	7.0%	172.4 / 5.4	57	M260V (ATG→GTG)	deoB	Phosphopentomutase
Reads supporting (aligned to +/- strand):  ref base A (21/32);  new base G (2/2);  total (23/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.26e-01

ACTATGCGTTAAAACCTTTTGGTAAAACTGTCTTAGATCATTTGAAAGACGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCATTATACGGTCATCGTCGTGATAAACCAGGTTATGCACAAGCAATTAAAG  >  USA300TCH1516_ALE/160448‑160717                                                                                                                                          |                                                                                                                                     aCTATGCGTTAAAACCTTTTGGTAAAACTGTCTTAGATCATTTGAAAGACGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATgg                                                                                                                                   <  2:264971/141‑1 (MQ=255)     tGCGTTAAAACCTTTTGGTAAAACTGTCTTAGATCATTTGAAAGACGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACgg                                                                                                                               >  2:102403/1‑141 (MQ=255)        gTTAAAACCTTTTGGTAAAACTGTCTTAGATCATTTGAAAGACGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTAt                                                                                                                            <  2:101608/141‑1 (MQ=255)         ttAAAACCTTTTGGTAAAACTGTCTTAGATCATTTGAAAGACGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATg                                                                                                                           >  2:66965/1‑141 (MQ=255)          tAAAACCGTTTGGTAAAACTGTGTTAGATCATGTGAAAGACGGTGGTTATGAGGTTAGTGCCAGCGGTAAAATTAATGACATTTATGCTGGTCAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATgg                                                                                                                          <  2:138910/141‑1 (MQ=255)           aaaaCCTTTTGGTAAAACTGTCTTAGATCATTTGAAAGACGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGa                                                                                                                         <  2:364590/141‑1 (MQ=255)               ccTTTTGGTAAAACTGTCTTAGATCATTTGAAAGACGGTGGTTATGATGTTATTGGCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCaa                                                                                                                     <  1:375697/141‑1 (MQ=255)                  tttGGTAAAACTGTCTTAGATCATTTGATAGACGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTCAAGGTGTAACAGAAGCCGATCGAACGAAGAATAACATGGCCGGAATGGTGCAAtgg                                                                                                                  <  2:351938/141‑3 (MQ=255)                     ggTAAAACTGTCTTAGATCATTTGAAAGACGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATtgatg                                                                                                               <  2:251230/141‑1 (MQ=255)                             tGTCTTAGATCATTTGAAAGACGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGt                                                                                                       <  2:209119/141‑1 (MQ=255)                             tGTCTTAGATCATTTGAAAGACGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGt                                                                                                       <  2:341271/141‑1 (MQ=255)                              gTCTTAGATCATTTGAAAGACGGTGGTTATGATGTTATTTCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGtt                                                                                                      <  1:279425/141‑1 (MQ=255)                                   aGATCATTTGAAAGACGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTaagaa                                                                                                 >  1:335487/1‑141 (MQ=255)                                    gATCATTTGAAAGACGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTaagaaa                                                                                                <  1:178584/141‑1 (MQ=255)                                     aTCATTTGAAAGACGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTaagaaag                                                                                               <  2:115384/141‑1 (MQ=255)                                        aTTTGAAAGACGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGAtt                                                                                            >  1:77624/1‑141 (MQ=255)                                        aTTTGAAAGACGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGAtt                                                                                            >  1:77625/1‑141 (MQ=255)                                            gAAAGACGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTcac                                                                                        >  1:337239/1‑141 (MQ=255)                                              aaGACGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAg                                                                                      >  2:273692/1‑141 (MQ=255)                                               aGACGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAgg                                                                                     <  1:213060/141‑1 (MQ=255)                                                  cGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTAt                                                                                  >  1:217321/1‑141 (MQ=255)                                                  cGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTAt                                                                                  >  1:300970/1‑141 (MQ=255)                                                   ggtggtTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTAtt                                                                                 <  2:347130/141‑1 (MQ=255)                                                     tggtTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACGTGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAg                                                                               >  2:127113/1‑141 (MQ=255)                                                     tggtTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACGTGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAg                                                                               >  2:127110/1‑141 (MQ=255)                                                         tATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGcttc                                                                           <  2:359673/141‑1 (MQ=255)                                                           tgatgTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGcttctt                                                                         <  1:111864/141‑1 (MQ=255)                                                                    tGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTtagt                                                                >  1:106534/1‑141 (MQ=255)                                                                     gCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTtagta                                                               <  2:134241/141‑1 (MQ=255)                                                                     gCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTtagta                                                               <  2:134261/141‑1 (MQ=255)                                                                     gCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTtagta                                                               >  2:279113/1‑141 (MQ=255)                                                                      ccATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTtagtag                                                              <  2:184350/141‑1 (MQ=255)                                                                         tCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACt                                                           <  1:323165/141‑1 (MQ=255)                                                                         tCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACt                                                           <  1:106540/141‑1 (MQ=255)                                                                          cGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACtt                                                          <  2:328348/141‑1 (MQ=255)                                                                           ggTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACttt                                                         >  1:212745/1‑141 (MQ=255)                                                                               aaaTTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATg                                                     >  1:171147/1‑141 (MQ=255)                                                                                 aTTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCa                                                   >  2:47557/1‑141 (MQ=255)                                                                                  ttAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGGCGGTATGGGCCGTCTTACTGAAAGTGATAAGAAAGGTTTCACAGGTAGTAGCTTCTTAAACGTAGTAGACTTTGATGCAt                                                  >  1:131470/1‑141 (MQ=255)                                                                                     aTGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCATtat                                               >  1:9683/1‑141 (MQ=255)                                                                                          aTTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCATTATACGGt                                          <  2:350768/141‑1 (MQ=255)                                                                                          aTTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCATTATACGGt                                          <  1:184157/141‑1 (MQ=255)                                                                                          aTTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGGATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCATTATACGGt                                          <  1:337995/141‑1 (MQ=255)                                                                                           tttATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCATTATACGGTc                                         <  2:114094/141‑1 (MQ=255)                                                                                                gatgGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCATTATACGGTCAtcgt                                    >  1:224588/1‑141 (MQ=255)                                                                                                   ggTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCATTATACGGTCATcgtcgt                                 >  2:310068/1‑141 (MQ=255)                                                                                                    gTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACGTGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCATTATACGGTCATCGTCGTg                                <  1:127110/141‑1 (MQ=255)                                                                                                    gTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACGTGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCATTATACGGTCATCGTCGTg                                <  1:127113/141‑1 (MQ=255)                                                                                                    gTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCATTATACGGTCATCGTCGTg                                <  1:27709/141‑1 (MQ=255)                                                                                                             tAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCATTATACGGTCATCGTCGTGATAAACCAg                       <  2:246173/141‑1 (MQ=255)                                                                                                             tAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCATTATACGGTCATCGTCGTGATAAACCAg                       <  1:66965/141‑1 (MQ=255)                                                                                                                    aGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCATTATACGGTCATCGTCGTGATAAACCAGGTTATGc                <  2:2697/141‑1 (MQ=255)                                                                                                                       ggTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCATTATACGGTCATCGTCGTGATAAACCAGGTTATGcaca             >  1:163574/1‑141 (MQ=255)                                                                                                                           cGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCATTATACGGTCATCGTCGTGATAAACCAGGTTATGCACAAGCa         <  1:206066/141‑1 (MQ=255)                                                                                                                                 aaGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCATTATACGGTCATCGTCGTGATAAACCAGGTTATGCACAAGCAATTaaa   <  2:363389/141‑1 (MQ=255)                                                                                                                                  agagTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCATTATACGGTCATCGTCGTGATAAACCAGGTTATGCACAAGCAATTAAAg  >  2:235710/1‑141 (MQ=255)                                                                                                                                  agagTAACATGAACGATATGGATGAATTGATGAAAATTGTTAAGAAAGGTTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCATTATACGGTCATCGTCGTGATAAACCAGGTTATGCACAAGCAATTAAAg  >  2:225243/1‑141 (MQ=255)                                                                                                                                          |                                                                                                                                     ACTATGCGTTAAAACCTTTTGGTAAAACTGTCTTAGATCATTTGAAAGACGGTGGTTATGATGTTATTGCCATCGGTAAAATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATGGACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTAAACTTAGTAGACTTTGATGCATTATACGGTCATCGTCGTGATAAACCAGGTTATGCACAAGCAATTAAAG  >  USA300TCH1516_ALE/160448‑160717

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: ‑