Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	401,399	A→C	11.4%	intergenic (‑184/‑57)	USA300HOU_RS01845 ← / → sutR	hypothetical protein/HTH‑type transcriptional regulator SutR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	401,399	0	A	C	11.4%	287.3 / 24.6	88	intergenic (‑184/‑57)	USA300HOU_RS01845/sutR	hypothetical protein/HTH‑type transcriptional regulator SutR
Reads supporting (aligned to +/- strand):  ref base A (42/36);  new base C (4/6);  total (46/42)
Fisher's exact test for biased strand distribution p-value = 5.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

TAAACAATTATGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGAAAGAATTACGAGCACGA  >  USA300TCH1516_ALE/401309‑401488                                                                                           |                                                                                          tAAACAATTATGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACaaa                                                                                           <  1:32632/91‑1 (MQ=255)  aaaCAATTATGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAat                                                                                          <  1:2389855/91‑1 (MQ=255)  aaaCAATTATGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAat                                                                                          <  1:279530/91‑1 (MQ=255)  aaaCAATTATGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAat                                                                                          <  1:2954731/91‑1 (MQ=255)   aaCAATTATGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAata                                                                                         >  1:222828/1‑91 (MQ=255)   aaCAATTATGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAata                                                                                         >  1:842326/1‑91 (MQ=255)   aaCAATTATGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGGGGATAATCATATTTTTTGGTGTAGATTTGACAAata                                                                                         >  1:221914/1‑91 (MQ=255)    aCAATTATGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAatat                                                                                        >  1:4093093/1‑91 (MQ=255)     cAATTATGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAACtata                                                                                       <  1:2971984/91‑1 (MQ=255)       aTTATGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAACtatatt                                                                                     <  1:2255860/91‑3 (MQ=255)       aTTATGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGt                                                                                     <  1:297760/91‑1 (MQ=255)        ttATGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGtt                                                                                    >  1:3842044/1‑91 (MQ=255)         tATGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTg                                                                                   >  1:115783/1‑91 (MQ=255)         tATGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTg                                                                                   <  1:967899/91‑1 (MQ=255)         tATGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTg                                                                                   <  1:2342608/91‑1 (MQ=255)          aTGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGt                                                                                  >  1:3776323/1‑91 (MQ=255)          aTGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGt                                                                                  >  1:3699852/1‑91 (MQ=255)          aTGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGt                                                                                  <  1:3355410/91‑1 (MQ=255)          aTGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGt                                                                                  >  1:986452/1‑91 (MQ=255)           tGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCTTACATAGGTGGATAATCATATTTTTTGGTGTAGTATTGACAACTATATTTGTc                                                                                 <  1:524837/91‑1 (MQ=255)           tGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTc                                                                                 <  1:1702151/91‑1 (MQ=255)            gACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCa                                                                                <  1:3572626/91‑1 (MQ=255)             aCTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAACTATATTTGTCaa                                                                               <  1:2892031/91‑1 (MQ=255)             aCTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAACTATATTTGTCaa                                                                               <  1:2891936/91‑1 (MQ=255)             aCTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAACTATATTTGTCaa                                                                               <  1:2891977/91‑1 (MQ=255)              cTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCaaa                                                                              >  1:3237789/1‑91 (MQ=255)              cTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCaaa                                                                              >  1:1965150/1‑91 (MQ=255)               ttGTAGGCGATGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTAGTCaaaa                                                                             >  1:2085837/1‑91 (MQ=255)                         tGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCatat                                                                   <  1:951070/91‑1 (MQ=255)                          gAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATc                                                                  <  1:4128441/91‑1 (MQ=255)                              tgtttgttTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCAttt                                                              <  1:3841965/91‑1 (MQ=255)                              tgtttgttTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCAttt                                                              <  1:3842008/91‑1 (MQ=255)                                tttgtttCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTAc                                                            >  1:1503173/1‑91 (MQ=255)                                   gtttCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAgt                                                         <  1:890967/91‑1 (MQ=255)                                     ttCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAgtgt                                                       <  1:355327/91‑1 (MQ=255)                                      tCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTa                                                      >  1:1161965/1‑91 (MQ=255)                                       cAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTaa                                                     <  1:3462087/91‑1 (MQ=255)                                       cAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTaa                                                     <  1:1893073/91‑1 (MQ=255)                                         aaaTGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAAtt                                                   <  1:1355451/91‑1 (MQ=255)                                         aaaTGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAAtt                                                   <  1:3513578/91‑1 (MQ=255)                                         aaaTGTCATACATAGGTGGACAATCATATTTTTTTGTGTGGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTagtt                                                   <  1:2222020/91‑4 (MQ=255)                                           aTGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTaa                                                 >  1:619676/1‑91 (MQ=255)                                           aTGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTaa                                                 <  1:1358719/91‑1 (MQ=255)                                           aTGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTaa                                                 <  1:1358529/91‑1 (MQ=255)                                             gTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAgg                                               >  1:2140980/1‑91 (MQ=255)                                             gTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAgg                                               >  1:2013779/1‑91 (MQ=255)                                               catacataGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAg                                             >  1:7992/1‑91 (MQ=255)                                                atacataGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGt                                            >  1:2407182/1‑91 (MQ=255)                                                atacataGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGt                                            >  1:1883131/1‑91 (MQ=255)                                                atacataGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGt                                            >  1:1182941/1‑91 (MQ=255)                                                atacataGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCACATCATTTACAGTGTAATTAAGGAGt                                            >  1:3850535/1‑91 (MQ=255)                                                 tacataGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGtt                                           >  1:2813973/1‑91 (MQ=255)                                                 tacataGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGtt                                           >  1:3426165/1‑91 (MQ=255)                                                  acataGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTg                                          <  1:3711493/91‑1 (MQ=255)                                                  acataGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTg                                          <  1:3711443/91‑1 (MQ=255)                                                  acataGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTg                                          <  1:3711154/91‑1 (MQ=255)                                                  acataGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTg                                          >  1:2676062/1‑91 (MQ=255)                                                  acataGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTg                                          >  1:1969992/1‑91 (MQ=255)                                                       ggTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCg                                     >  1:2012937/1‑91 (MQ=255)                                                       ggTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCg                                     >  1:4074026/1‑91 (MQ=255)                                                         tGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGAt                                   >  1:46330/1‑91 (MQ=255)                                                          ggATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGAtg                                  >  1:552766/1‑91 (MQ=255)                                                          ggATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGAtg                                  >  1:3891179/1‑91 (MQ=255)                                                          ggATAATCATATTTTTTGGTGGAGAATTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGAtg                                  <  1:547725/91‑1 (MQ=255)                                                           gATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGAtgt                                 >  1:896156/1‑91 (MQ=255)                                                             tAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGc                               >  1:201431/1‑91 (MQ=255)                                                             tAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGc                               >  1:1418796/1‑91 (MQ=255)                                                             tAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGc                               <  1:1930312/91‑1 (MQ=255)                                                             tAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTCTAATTAAGGAGTTGATGCGATGTGc                               >  1:3871932/1‑91 (MQ=255)                                                              aaTCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCg                              <  1:575687/91‑1 (MQ=255)                                                              aaTCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCg                              >  1:1968554/1‑91 (MQ=255)                                                              aaTCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCg                              <  1:2030381/91‑1 (MQ=255)                                                                  atatTTTTTGGTCTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGCAAt                          >  1:3209137/1‑91 (MQ=255)                                                                     ttttttGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGa                       >  1:3708607/1‑91 (MQ=255)                                                                     ttttttGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGa                       >  1:3708006/1‑91 (MQ=255)                                                                       ttttGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGAtt                     <  1:1721092/91‑1 (MQ=255)                                                                        tttGGTGTAGATTTGTCAAATATAGTTGTCAAGAAGACGCATATCATTTGCAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTg                    <  1:1995312/91‑1 (MQ=255)                                                                         ttGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGa                   <  1:1620848/91‑1 (MQ=255)                                                                          tGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGaa                  <  1:1102086/91‑1 (MQ=255)                                                                           ggTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGaaa                 >  1:2148404/1‑91 (MQ=255)                                                                           ggTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGaaa                 >  1:1446644/1‑91 (MQ=255)                                                                           ggTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGaaa                 >  1:749740/1‑91 (MQ=255)                                                                            gtgtAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGAAAg                >  1:1237930/1‑91 (MQ=255)                                                                               tAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGAAAGAAt             <  1:990743/91‑1 (MQ=255)                                                                               tAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGAAAGAAt             >  1:309931/1‑91 (MQ=255)                                                                               tAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGAAAGAAt             <  1:1573128/91‑1 (MQ=255)                                                                                 gATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGAAAGAATTa           <  1:3524410/91‑1 (MQ=255)                                                                                 gATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGAAAGAATTa           <  1:145599/91‑1 (MQ=255)                                                                                   tttGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGAAAGAATTACg         <  1:2050238/91‑1 (MQ=255)                                                                                    ttGACAACTATATTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGAAAGAATTACGa        >  1:3163481/1‑91 (MQ=255)                                                                                    ttGACAACTATATTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGAAAGAATTACGa        >  1:2762268/1‑91 (MQ=255)                                                                                     tGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGAAAGAATTACGAg       >  1:2382156/1‑91 (MQ=255)                                                                                      gACAACTATATTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGAAAGAATTACGAGc      >  1:3637504/1‑91 (MQ=255)                                                                                      gACAACTATATTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGAAAGAATTACGAGc      >  1:3637451/1‑91 (MQ=255)                                                                                       aCAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGAAAGAATTACGAGCa     <  1:2086840/91‑1 (MQ=255)                                                                                        cAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGAAAGAATTACGAGCAc    >  1:962410/1‑91 (MQ=255)                                                                                          aaTATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGAAAGAATTACGAGCACga  <  1:1396229/91‑1 (MQ=255)                                                                                          aaTATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGAAAGAATTACGAGCACga  <  1:1396946/91‑1 (MQ=255)                                                                                          aaTATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGAAAGAATTACGAGCACga  >  1:1549304/1‑91 (MQ=255)                                                                                           |                                                                                          TAAACAATTATGACTTGTAGGCGTTGAGGTGTTTGTTTCAAAATGTCATACATAGGTGGATAATCATATTTTTTGGTGTAGATTTGACAAATATAGTTGTCAAAAAGACGCATATCATTTACAGTGTAATTAAGGAGTTGATGCGATGTGCGTAATCGATTGAAAGAATTACGAGCACGA  >  USA300TCH1516_ALE/401309‑401488

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