Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	923,858	T→C	6.6%	W53R (TGG→CGG)	lipA_1 →	Lipoyl synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	923,858	0	T	C	6.6%	178.4 / 2.2	68	W53R (TGG→CGG)	lipA_1	Lipoyl synthase
Reads supporting (aligned to +/- strand):  ref base T (34/29);  new base C (3/2);  total (37/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.23e-01

GGAAATATTACGTAAACCGGATTGGTTGAAAATAAAATTAAATACCAACGAAAACTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGATTTAAATGA‑GCCTGAACGTGTAGCTGAATCAGTTGAATT  >  USA300TCH1516_ALE/923719‑923997                                                                                                                                            |                                                                                                                                              ggAAATATTACGTAAACCGGATTGGTTGAAAATAAAATTAAATACCAACGAAAACTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTg                                                                                                                                              >  1:663648/1‑141 (MQ=255) ggAAATATTACGTAAACCGGATTGGTTGAAAATAAAATTAAATACCAACGAAAACTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTg                                                                                                                                              >  1:546355/1‑141 (MQ=255)         tACGTAAACCGGATTGGTTGAAAATAAAATTAAATACCAACGAAAACTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑c                                                                                                                                     >  1:613119/1‑141 (MQ=255)          aCGTAAACCGGATTGGTTGAAAATAAAATTAAATACCAACGAAAACTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑cg                                                                                                                                    >  2:48586/1‑141 (MQ=255)          aCGTAAACCGGATTGGTTGAAAATAAAATTAAACACCAACGAAAACTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑cg                                                                                                                                    <  1:222858/141‑1 (MQ=255)           cGTAAACCGGATTGGTTGACAATAAAATTCAATACCAACGAAAACTATACAGGCCTTAAGACGATGATGAGGGCAAAAAATCTTAATACTATAAGCGAAGAAGATAAATGTACTAATATACATAAATGTTGGGGTGCA‑cgt                                                                                                                                   >  2:596538/1‑141 (MQ=255)             tAAACCGAGTTGGTTGAAAATAAAATTAAATACCAACGAAAACTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑cgtcg                                                                                                                                 <  2:525501/141‑1 (MQ=255)                  cgtaTTGGTTTAAAATAAAACTAAAAACCCACGTGAACTAGAATCCACATAAGAGGCTGAGCAGGCAAAAAAATCGTAATACCGTATTTGAAGAAGCTAGATATCATCATATACATGATTGTTGGGGTGCA‑CGTCGTACAg                                                                                                                            <  2:276561/138‑1 (MQ=255)                    gATTGGTTGAAAATAAAATGAAATACCAACGAAAACTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCg                                                                                                                          <  2:121102/141‑1 (MQ=255)                     aTTGGTTGAAAATAAAATTAAATACCAACGAAAACTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGa                                                                                                                         <  1:344788/141‑1 (MQ=255)                                  aaaatTAAATACCAACGAAAACTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGAtttt                                                                                                            <  2:454191/141‑1 (MQ=255)                                  aaaatTAAATACCAACGAAAACTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATGTATGAtttt                                                                                                            >  1:656342/1‑141 (MQ=255)                                     atTAAATACCAACGAAAACTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTCGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAg                                                                                                          >  2:629167/1‑140 (MQ=255)                                     atTAAATACCAACGAAAACTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTCGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAg                                                                                                          >  2:629169/1‑140 (MQ=255)                                     atTAAATACCAACGAAAACTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTCGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAg                                                                                                          <  1:629167/140‑1 (MQ=255)                                     atTAAATACCAACGAAAACTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTCGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAg                                                                                                          <  1:629169/140‑1 (MQ=255)                                       tAAATACCAACGAAAACTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGAGTGCA‑CGTCGAACAGCGACCTTTATGATTTTAGGTg                                                                                                       >  2:231906/1‑141 (MQ=255)                                         aaTACCAACGAAAACTATACAGGACTTAAGAAGATGATGAGGGATAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGcc                                                                                                     >  2:422782/1‑141 (MQ=255)                                          aTACCAACGAAAACTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATCCTTTAGGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCg                                                                                                    <  1:563119/141‑1 (MQ=255)                                          aTACCAACGAAAACTATACAGGACTTAAGAAGATGATGAGGGAAAAAAAACTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGAGCCg                                                                                                    >  2:301317/1‑141 (MQ=255)                                              cAACGAAAACTAGACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATg                                                                                                <  1:313117/141‑1 (MQ=255)                                                      aCTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAagag                                                                                        >  2:353841/1‑141 (MQ=255)                                                       cTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAGGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTAAGGTCCCGTATGTACAGGAGc                                                                                       >  2:188103/1‑141 (MQ=255)                                                       cTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGc                                                                                       >  1:473486/1‑141 (MQ=255)                                                       cTATACAGGACTTAAGAAGATGATGAGCAAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGTGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGc                                                                                       <  1:381174/141‑1 (MQ=255)                                                          taCAGGACTTAAGAAGATGATGAGGTAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTg                                                                                    <  1:376077/141‑1 (MQ=255)                                                          taCAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTTTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGACTTTAGGTGCCGTATGTACAAAAGCttt                                                                                    >  2:25823/1‑140 (MQ=255)                                                          taCAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTg                                                                                    <  2:734268/141‑1 (MQ=255)                                                              ggACTTAAAAAAATGAGTAGGGAAAAAAATCTTAATACTGTATGGGAAGAAGCTAAATGTCCTAATATACAGGAATGTTGGGTTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGt                                                                                <  2:370375/141‑1 (MQ=255)                                                                acgtAAGTAGATGATGAGGGCAGGAAATCTGAATACTGTATGTGAAGAAGCGAAATGTCCTCAGATACAGGAATGTTGGGGTGCA‑CATCGTACAGCGACAGTTATGATTTTATGTGCCGTATGTACAAGAGCTTGTCGttt                                                                              <  1:501727/138‑1 (MQ=255)                                                                   tAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTtg                                                                           <  2:764769/141‑1 (MQ=255)                                                                   tAAGAAAATGAAGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTtg                                                                           <  1:730708/141‑1 (MQ=255)                                                                    aagaagATGATGAGGGAAAAAAATCTTAATACGGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTtgt                                                                          >  2:493987/1‑141 (MQ=255)                                                                          atgatgAGTGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGtt                                                                    <  1:592941/141‑1 (MQ=255)                                                                           tgatgaGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGAGGTGCA‑CGTCGTACAGCGACATGTATGATTTTAGGGGCCGGATGTACAAGAGCTTGTCGTTTTTGTGCGGTTa                                                                   >  2:733778/1‑141 (MQ=255)                                                                           tgatgaCGGAAAAAAATCCTAATACTGTATGTGAAGAAGCTAAATGTCCTAATAGACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTa                                                                   <  1:259144/141‑1 (MQ=255)                                                                           agatgaGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTACGATTTTAAGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTa                                                                   <  2:149817/140‑1 (MQ=255)                                                                           aaagtaGGGAAAAAAATCTTAATCCTGTATGTGAAGAAGCTAAAAGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTa                                                                   <  1:315903/136‑1 (MQ=255)                                                                             atgaGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAg                                                                 >  1:128119/1‑141 (MQ=255)                                                                              tgaGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGa                                                                >  1:227252/1‑141 (MQ=255)                                                                              tgaGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGAGGTGCC‑CGTCGTACAGCGACCTTTATGATTGTAGTTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAgg                                                                >  2:156167/1‑140 (MQ=255)                                                                               gaGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGAc                                                               <  2:689399/141‑1 (MQ=255)                                                                                 gggAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGTTTAAGGCAg                                                             <  2:452209/141‑1 (MQ=255)                                                                                   gAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGt                                                           <  1:392465/141‑1 (MQ=255)                                                                                                      tATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGGCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGAtt                                        <  2:128750/141‑1 (MQ=255)                                                                                                      tATGTGAAGAAGCTAAATGTCACATAGCACATGAATGATCGCGTGTG‑CTTTGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGAtt                                        <  1:560333/141‑1 (MQ=255)                                                                                                          tgAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGCGCATGGCGGTTGTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGATTTaaa                                    >  1:59323/1‑141 (MQ=255)                                                                                                           gaagaaGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGGGCTTGTCGTTGTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGATTCAAAt                                   >  2:437106/1‑141 (MQ=255)                                                                                                             agaagCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGATTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGATTTAAATGa                                 >  2:75691/1‑141 (MQ=255)                                                                                                                aggtAAATCTCCTAATAGACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGGTTTAAATGA‑Gcc                             <  2:164749/138‑1 (MQ=255)                                                                                                                agCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAAGGAACTTGATTTAAATgtgtc                              >  2:409278/1‑137 (MQ=255)                                                                                                                    aaaTGTCCTAATATACATGGGTACCAAGATGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGATTTAAATGA‑GCCTGaa                         >  1:375323/1‑141 (MQ=255)                                                                                                                     aaTGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGATTTAAATGA‑GCCTGAAc                        >  2:479225/1‑141 (MQ=255)                                                                                                                      aTGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGATTTAAATGA‑GCCTGAACg                       <  2:140563/141‑1 (MQ=255)                                                                                                                       tGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGATTTAACTGA‑GCCTGAAccg                      >  1:705221/1‑139 (MQ=255)                                                                                                                          ccTACTATACATAAATGTTGAGGTCCA‑CGTCGTACAGCGACACTTCTGATCTTAGGTGATTGATCGACAAGAGCTTGTCGTTTTTGTGGGGTTAAGAACAGTTTACCTAATGAACTTGATTTAAATTA‑GCCTGAACGTGTa                   >  2:319182/1‑141 (MQ=255)                                                                                                                            tAATCTACATGAATGTTGGGGTGAAGAATCG‑GCATGGGTATTGATCATTTTTGGTCCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGATTTAAATGA‑GCCTGAACGTGTAGc                 <  1:293798/141‑1 (MQ=255)                                                                                                                            caaTATAACTGAATGTTGGGTTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGATTTAAATGA‑GCCTGAACGTGTAGc                 <  1:596538/140‑1 (MQ=255)                                                                                                                             aaTATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGATTTAAATGA‑GCCTGAACGTGTAGCt                >  2:297920/1‑141 (MQ=255)                                                                                                                               tataCATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGATTTAAATGA‑GCCTGAACGTGTAGCTGa              >  1:381568/1‑141 (MQ=255)                                                                                                                                  aCATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGATTTAAATGA‑GCCTGAACGTGTAGCTGAATc           >  2:121495/1‑141 (MQ=255)                                                                                                                                  aCATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGATTTAAATGA‑GCCTGAACGTGTAGCTGAATc           >  2:268420/1‑141 (MQ=255)                                                                                                                                     tGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGCGTTAAATGA‑GCCTGGACGTGTAGCTGAATCAgg        >  1:667564/1‑140 (MQ=255)                                                                                                                                        aTGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGATTTAAATGA‑GCCTGAACGTGTAGCTGAATCAGTTGa     <  1:48586/141‑1 (MQ=255)                                                                                                                                         tGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGATTTAAATGA‑GCCTGAACGTGTAGCTGAATCAGTTGat    >  2:456280/1‑140 (MQ=255)                                                                                                                                         tGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGATTTAAATGA‑GCCTGAACGTGTAGCTGAATCAGTTGaa    >  2:456360/1‑141 (MQ=255)                                                                                                                                         tGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGATTTAAATGA‑GCCTGAACGTGTAGCTGAATCAGTTGaa    >  2:111137/1‑141 (MQ=255)                                                                                                                                          gTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATGTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGATTTAAATGA‑GCCTGAACGTGTAGCTGAATCAGTTGAAt   >  1:184387/1‑141 (MQ=255)                                                                                                                                           gtGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGCACAAGAGCTTGTCGTTTTTGTGCGGCTAAGACAGGTTTACCTAATGAACTTCATTTAACTGATTGCTG‑GCGTTTAGCTGAATCAGCTGAAtt  <  1:570663/140‑1 (MQ=255)                                                                                                                                            |                                                                                                                                              GGAAATATTACGTAAACCGGATTGGTTGAAAATAAAATTAAATACCAACGAAAACTATACAGGACTTAAGAAGATGATGAGGGAAAAAAATCTTAATACTGTATGTGAAGAAGCTAAATGTCCTAATATACATGAATGTTGGGGTGCA‑CGTCGTACAGCGACATTTATGATTTTAGGTGCCGTATGTACAAGAGCTTGTCGTTTTTGTGCGGTTAAGACAGGTTTACCTAATGAACTTGATTTAAATGA‑GCCTGAACGTGTAGCTGAATCAGTTGAATT  >  USA300TCH1516_ALE/923719‑923997

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑