Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,227,320	T→G	23.9%	I40L (ATT→CTT)	atpB ←	ATP synthase subunit a

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,227,320	0	T	G	23.9%	81.6 / 28.5	64	I40L (ATT→CTT)	atpB	ATP synthase subunit a
Reads supporting (aligned to +/- strand):  ref base T (23/24);  new base G (7/8);  total (31/33)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.62e-01

CAGCGTTACTGCTAAGAAGTGGAATTGACCACCTTTTTTCCAAGCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGCGGGGATTTGTGATCCATAATCTCACCTCTTTCTTAATTTA  >  USA300TCH1516_ALE/2227180‑2227460                                                                                                                                             |                                                                                                                                             cAGCGTTACTGCTAAGAAGTGGCATTGACCCCCTTTTTTCCAAGCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAAt                                                                                                                                              <  2:734709/141‑1 (MQ=255) cAGCGTTACTGCTAAGAAGTGGAATTGACCACCTTTTTTCCAAGCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTGGCCGGTTGGTCTTTTTTTCCAACTACTCGAACAAAt                                                                                                                                              >  1:679816/1‑141 (MQ=255)    cGTTACTGCTAAGAAGTGGAATTGACCACCTTTTTTCCAAGCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTTCAAATGAt                                                                                                                                           >  1:523634/1‑141 (MQ=255)    cGTTACTGCTAAGAAGTGGAATTGACCACCTTTTTTCCAAGCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGAt                                                                                                                                           >  1:199140/1‑141 (MQ=255)                    tGGAATTGACCACCTTTTTTCCAAGCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTTTAATTACTCTTACAAATGATAGCAAGAGGAAAAACa                                                                                                                           >  2:164195/1‑141 (MQ=255)                    tGGAATTGACCACCTTTTTTCCAAGCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATTATAGCAAGTAGAAAAACa                                                                                                                           <  2:230244/141‑1 (MQ=255)                    tGGAATTGACCACCTTTTTTCCAAGCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAAGGATAGCAAGTAGAAAAACa                                                                                                                           <  1:650559/141‑1 (MQ=255)                    gggAATTGACCACCTTTTTTCCAAGCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAAGGATAGCAAGTAGAAAAACa                                                                                                                           <  1:214046/140‑1 (MQ=255)                        aTTGACCACCTTTTTTCCAAGCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAAGTGGAAAAACAAGaa                                                                                                                       >  2:270892/1‑141 (MQ=255)                        aTTGACCACCTTTTTTCCAAGCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAAGGAAAGCAAGTAGAAAAACAAGaa                                                                                                                       >  2:478120/1‑141 (MQ=255)                          tGACCACCTTTTTTCCAAGCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAAGGATAGCAAGTAGAAAAACAAGAAAc                                                                                                                     >  1:653526/1‑141 (MQ=255)                            accaccTTTTTTCCAAGCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTGGCCAGTTGGTATTTTTTACAAATGACGCTTAGAACTGATACGAAGTACAACAACAAAAAACGc                                                                                                                   >  1:694399/1‑141 (MQ=255)                              ccccTTTTTGCCAAGCCATGTTACCTTCAATGATTCCACTCACGAAATCAAAAATCCATTCAACGATATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGACAGCAAGTAGAAAAACAAGAAACGCCg                                                                                                                 <  1:266147/139‑1 (MQ=255)                               accTTTTTTCCAAGCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGt                                                                                                                >  1:100886/1‑141 (MQ=255)                               accTGTTTTCCAAGCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCATACAAATGATAGCAAGTAGAAGAACAAGAAACGCCGt                                                                                                                >  1:555524/1‑141 (MQ=255)                                ccTTTTTTCCAAGCCATGTTACCTTCGATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAAGGATAGCAAGTAGAAAAACAAGAAACGCCGTa                                                                                                               <  2:40130/141‑1 (MQ=255)                                   tttttCCAAGGTATTTTAGCTACAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGGTGGTCCTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACa                                                                                                            <  2:316726/141‑1 (MQ=255)                                   tttttCCAAGCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACa                                                                                                            <  1:67485/141‑1 (MQ=255)                                   ttgttCCAAGCCATGTTACCTGCCATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTATTCAAATTCCGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACa                                                                                                            <  1:306486/138‑1 (MQ=255)                                     tttCCAAGCCATGGTAGCTCCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCGAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAg                                                                                                          <  2:502581/141‑1 (MQ=255)                                      ttCCAAGCCATGTTACCTTCAATGATCCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGt                                                                                                         <  2:598099/141‑1 (MQ=255)                                       tCCAAGCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAGAAACAAGAAACGCCGTAACAAGTa                                                                                                        >  2:265943/1‑141 (MQ=255)                                         cAAGCCATGTTACCTTCAATGATTCCCCTCTCGAAATCAAAAATCCATTCAACGGAATTTTGTTTGCCAGTTGGTCTTTTTTTCAATTTTCCCGTACAAAGGATAGCAAGTAGAAAAACAAGAAGCGCCGTAACAAGTatc                                                                                                      >  1:21863/1‑141 (MQ=255)                                          aaGCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGGTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTatca                                                                                                     <  2:164755/141‑1 (MQ=255)                                           aGCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATACATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTatcat                                                                                                    <  1:195154/141‑1 (MQ=255)                                            gCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTatcatc                                                                                                   <  1:701106/141‑1 (MQ=255)                                                      cTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAGGAAGAAAATCAAGAAACGCCGTAACAAGTATCATCAATATACttt                                                                                         >  1:5940/1‑140 (MQ=255)                                                         cAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATa                                                                                      <  2:776346/141‑1 (MQ=255)                                                                tCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAAGGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGaa                                                                               >  2:375296/1‑141 (MQ=255)                                                                tCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAAGGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGaa                                                                               >  1:288326/1‑141 (MQ=255)                                                                 ccccTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCCATATACTTGATAAATTGaaa                                                                              >  1:238017/1‑141 (MQ=255)                                                                 ccccTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGaaa                                                                              >  1:600852/1‑141 (MQ=255)                                                                     tCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTATGCGTACAAATGATAGCAAGTAGCACAACAAGAAACGCCTTAACAAGTATCATCAATATACTTGGTAAATTGAAAACgc                                                                          >  2:2054/1‑140 (MQ=255)                                                                       aCGAAATCAAAAATCCATTCAACTAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGata                                                                        <  2:535420/141‑1 (MQ=255)                                                                       aCGAAATCAAAAATCCATCCAACGAAATTTTATTTGCCAGTTGGTCGTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGata                                                                        <  2:535527/141‑1 (MQ=255)                                                                              cAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGAATCATCAATATACTTGATAAATTGAAAACGATATCAAAAc                                                                 >  1:553511/1‑141 (MQ=255)                                                                                aaaaTCCATTCCACTACATTGTGTTAGCCCGTTGTCCTTTTTTTCAAATTACCCGTACAAATGATAGCAAATAGAAAAACAAGAAAAGCAGTAACAAGTATCATCATTATACTTGATAAATTGAAAACGATATCACAACCg                                                               <  2:633418/141‑1 (MQ=255)                                                                                  aaTCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGGTAAATTGAAAACGATATAAAAACCGaa                                                             >  2:449000/1‑141 (MQ=255)                                                                                  aaTCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGaa                                                             >  1:527710/1‑141 (MQ=255)                                                                                   aTCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAAGGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAAt                                                            <  2:160220/141‑1 (MQ=255)                                                                                     ccATTCAACGAAAGTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAAGGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATaa                                                          <  2:102835/141‑1 (MQ=255)                                                                                        ttCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACTCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAAtt                                                       >  1:744203/1‑141 (MQ=255)                                                                                                   tttgtttgCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATAAACTTGATAAATTGAAAAGGATATAAAAACCGCAAAAATTCAAACTCACGa                                            >  2:376271/1‑141 (MQ=255)                                                                                                    ttgtttgCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAAGGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAg                                           >  1:18138/1‑141 (MQ=255)                                                                                                     tgtttgCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGc                                          <  1:657884/141‑1 (MQ=255)                                                                                                     tgtttgCCAGTTGGTCTTTTTTTCAAATTACGCGTAAAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGc                                          <  1:588879/141‑1 (MQ=255)                                                                                                      tttggCCAGTTGGTGTTTTTTTTAAATTACTCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGCg                                         <  2:639523/137‑1 (MQ=255)                                                                                                      gtttgCCAGTTAGTCGTGTTTTCAAATGACTCGTACAAACGATAGCAAGTAGAAAAACAAGAAACGTCGTAACAATTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGCg                                         <  2:59652/141‑1 (MQ=255)                                                                                                           ccAGTCGATCTCTTTTTCAAATAACGCGTACAAATGAAAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGCGGGGAt                                    <  2:673625/141‑1 (MQ=255)                                                                                                           ccAGATTGTCTTTTTTTCAAATTCCGCGTACAAAGGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAAATCCAACTCACGAGCGGGGAt                                    <  1:477164/141‑1 (MQ=255)                                                                                                            cAGTTGGTCTTTTTTTCAAATTACGCGTAAAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGCGGGGAtt                                   <  2:725897/141‑1 (MQ=255)                                                                                                                     tttttttCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATACATTGACTGCAATATCAAAACCGAATAAATTCCAACTCACGAGCGGGGGTTTGTGATCCa                          >  1:739393/1‑141 (MQ=255)                                                                                                                     tttttttCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGCGGGGATTTGTGATCCa                          >  1:34138/1‑141 (MQ=255)                                                                                                                      ttttttCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATCTCAAAACCGAATAAATTCCAACTCACGAACGGGGATTTGTGATCCAt                         >  1:593674/1‑141 (MQ=255)                                                                                                                         tttCAAATTACGGGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGCGGGGATTTGTGATCCATAAt                      <  1:74319/141‑1 (MQ=255)                                                                                                                             acaTTACGCGTACAATGGATAGCAAGAAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAATGATATCAAAACCGTATAAATTCCAACTCACGAGCGGGAATTTGTGATCCATAATCTCa                  <  1:478120/139‑1 (MQ=255)                                                                                                                             aaaTTACGCGTACAAATGCTAGCAAGTACAAAAAAAAGAAACGCCCTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGCGGGGATTTGTGATCCATAATCTCa                  <  1:19313/141‑1 (MQ=255)                                                                                                                             aaaTTACGCGTACAAATGATAGCAAGCAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGCGGGTATTTGTGATCCATAATCTCa                  <  1:478149/141‑1 (MQ=255)                                                                                                                             aaaTTACGCGTACAAAGGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGCGGGGATTTGTGATCCATAATCTCa                  <  2:653526/141‑1 (MQ=255)                                                                                                                              aaTTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGCGGGGATTTGTGATCCATAATCTAAc                 >  1:488643/1‑141 (MQ=255)                                                                                                                              aaTTACGCGTACAAAAGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGGATCATCAATATACTTGATAATTTGAACTCGATATCTAAACCGAATAAATTCCAACTCACGAGCGTGGATTTGTGATCCATAAtgcgac                 >  2:102348/1‑136 (MQ=255)                                                                                                                                  aCGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGCGGGGATTTGTGATCCATAATCTCACctct             <  1:650971/141‑1 (MQ=255)                                                                                                                                    gcgTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGCGGGGATTTGTGATCCATAATCTCACCtcttt           >  1:736835/1‑141 (MQ=255)                                                                                                                                     cgTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGCGGGGATTTGTGATCCATAATCTCACCtctttc          <  1:120383/141‑1 (MQ=255)                                                                                                                                         cAAAGGATAGCAAGTCGAACAAAAAGTAAAGCCGTAACAATTAGCAGCAAAATACTTGAGAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGCGGGGATTTGTGATCCATAATCTCACCTCTTTCTTaa      >  2:746792/1‑141 (MQ=255)                                                                                                                                            aTGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGCGGGGATTTGTGATCCATAATCTCACCTCTTTCTTAattt   >  1:403700/1‑141 (MQ=255)                                                                                                                                             tGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGCGGGGATTTGTGATCCATAATCTCACCTCTTTCTTAatttt  >  1:680903/1‑140 (MQ=255)                                                                                                                                             tGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGCGGGGATTTGTGATCCATAATCTCACCTCTTTCTTAatttt  >  1:80851/1‑140 (MQ=255)                                                                                                                                             |                                                                                                                                             CAGCGTTACTGCTAAGAAGTGGAATTGACCACCTTTTTTCCAAGCCATGTTACCTTCAATGATTCCCCTCACGAAATCAAAAATCCATTCAACGAAATTTTGTTTGCCAGTTGGTCTTTTTTTCAAATTACGCGTACAAATGATAGCAAGTAGAAAAACAAGAAACGCCGTAACAAGTATCATCAATATACTTGATAAATTGAAAACGATATCAAAACCGAATAAATTCCAACTCACGAGCGGGGATTTGTGATCCATAATCTCACCTCTTTCTTAATTTA  >  USA300TCH1516_ALE/2227180‑2227460

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: ‑