Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,223,916	A→T	6.2%	L420* (TTA→TAA)	atpA ←	ATP synthase subunit alpha

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,223,916	0	A	T	6.2%	194.4 / 2.1	67	L420* (TTA→TAA)	atpA	ATP synthase subunit alpha
Reads supporting (aligned to +/- strand):  ref base A (32/30);  new base T (3/2);  total (35/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTCTGCCCAGTGGTTTAACTCGTCTTCAAAACGTGTGATATCTACAACTGGAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCTAAGTCAAGACGTAACGTACCAGCAACTTTCTTCATTGC  >  USA300TCH1516_ALE/2223779‑2224055                                                                                                                                          |                                                                                                                                            aTTCTGCCCAGTGGTTTAACTCGTCGTCAAAACGTGTGATATCTACAACTGGAATACACCCCAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAg                                                                                                                                           >  2:498873/1‑140 (MQ=255)  ttCTGCCCAGTGGTTTAACTCGTCTTCAAAACGTGTGATATCTACAACTGGAATATCATCTAAATATCCTTTTGTTGATGCATAAATAATCAAAACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGa                                                                                                                                          >  2:397584/1‑140 (MQ=255)      gCCCAGTGGTTTAACTCGTCTTCAAAACGTGTGATATCTACAACTGGAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTc                                                                                                                                      >  1:193734/1‑140 (MQ=255)      gCCCAGTGGTTTAACTCGTCTTCAAAACGTGTGATATCTACAACTGGAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTc                                                                                                                                      >  2:173868/1‑140 (MQ=255)      gCCCAGTGGATTAACTCGTCTTCAAAACGTGTGATATCTACAACTGGAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTc                                                                                                                                      >  1:403744/1‑140 (MQ=255)           gTGGTTTAACTCGTCTTCAAAACGTGTGATATCTACAACTGGAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGAGTGCGACGGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAg                                                                                                                                 <  1:17877/140‑1 (MQ=255)            tGGTTTAACTCGTCTTCAAAACGTGTGATATCTACAACTGGAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGt                                                                                                                                <  1:494613/140‑1 (MQ=255)            tGGTTTAACTCGTCTTCAAAACGTGTGATATCTACAACTGGAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGt                                                                                                                                >  2:449480/1‑140 (MQ=255)                 tAACTCGTCTTCAAAACGTGTGATATCTACAACTGGAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGtt                                                                                                                           >  2:519987/1‑140 (MQ=255)                       gTCTTTAAAACGTGTGATATCTACAACTGGAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCAc                                                                                                                     <  1:504445/140‑1 (MQ=255)                         cTTCAAAACGTGTGATATCTACAACTGCAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGt                                                                                                                   <  1:335240/140‑1 (MQ=255)                            taaaaCGTGTGATATCTTCAACTGGCATATCATCTAAATTTCCTTTTGTTAATGCATAAATAATCAACACTTGGTTTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCt                                                                                                                <  1:338521/139‑1 (MQ=255)                            cAAAACGTGTGATATCTACAACTGGAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCt                                                                                                                >  1:116001/1‑140 (MQ=255)                              aaaCGTGTGATATCTACAACTGGAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCAACTGGTAATGGATTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTaa                                                                                                              >  1:145320/1‑140 (MQ=255)                                atgtgtTATATCTACAACTGGAATATTATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTTGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAAtt                                                                                                            <  1:548381/138‑1 (MQ=255)                                aCGTGTGATATCTACCACTGGAATATCATCTAAAAATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAAtt                                                                                                            <  2:19006/140‑1 (MQ=255)                                 cGTGTGATATCTACAACTGGAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAAttt                                                                                                           <  2:486278/140‑1 (MQ=255)                                    gtgATATCTACAACTGGAATATCATCTAAATATCCTTTTTTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACt                                                                                                        <  1:447507/140‑1 (MQ=255)                                     tgATATCTACAACTGGAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACtt                                                                                                       <  2:254419/140‑1 (MQ=255)                                         atCTACAACTGGAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACATTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAg                                                                                                   <  1:218700/140‑1 (MQ=255)                                         atCTACAACTGGAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAg                                                                                                   <  1:543164/140‑1 (MQ=255)                                                aCTGGAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATtc                                                                                            >  1:394017/1‑140 (MQ=255)                                                aCTGGAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATtc                                                                                            >  1:84537/1‑140 (MQ=255)                                                  tGGAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTAAACAGTACGTTTACCACGTTCTAATTTACTTGAAGTAAATtcat                                                                                          >  1:496252/1‑140 (MQ=255)                                                   ggAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATtcatc                                                                                         >  2:248464/1‑140 (MQ=255)                                                     aaTATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCaa                                                                                       >  1:528539/1‑140 (MQ=255)                                                              tAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAAc                                                                              <  1:549711/140‑1 (MQ=255)                                                              ataaTAACCTTTTGTTAATCTATAAATAACCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACATTACGTTTACCACGTTCTAATTTCCTTGCAGTAAATTCATCAAGGTCTGAAc                                                                              <  2:71144/138‑1 (MQ=255)                                                               aaaTATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAAcc                                                                             <  2:191325/140‑1 (MQ=255)                                                                 atatCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGa                                                                           >  2:439806/1‑140 (MQ=255)                                                                       ttttGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATtgtg                                                                     <  2:58634/140‑1 (MQ=255)                                                                           gTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGACTGAACCGAATTGTGCaaa                                                                 >  1:438023/1‑140 (MQ=255)                                                                            ttAATGCATAAATAATCAACAGTTGGTGTTCGACTGGTAATGGTTTGTATTGATATTGTTTTAAGACTTCAACAGTAAGTTTACCACGTTCTAATTTACTTGCAATAAATTCATCAAGGTCTGACCAGAAGTGTTCAAAt                                                                >  2:202357/1‑140 (MQ=255)                                                                            ttAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTGAGCAGTACGTTTAGCACGTTCTAATTTACTTGCAGTAAAGTCATCAAGGTCAGAACCGACTTGTGCAAAt                                                                >  2:410186/1‑140 (MQ=255)                                                                                   ataaataaTCAACACTTGGTGTTCGACTTGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCaa                                                         <  1:97705/140‑1 (MQ=255)                                                                                    taaataaTCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAg                                                        <  1:439806/140‑1 (MQ=255)                                                                                     aaataaTCAAGACTTGGTGTTCGAGTGGTCATGGTCCGGCCGGTGCGTGTTTTAAAACTGCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAgg                                                       >  1:402755/1‑139 (MQ=255)                                                                                       ataatCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTtc                                                     <  1:221717/140‑1 (MQ=255)                                                                                         aatCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTtctc                                                   >  1:362227/1‑140 (MQ=255)                                                                                          atCAACACTTGGTGTTGGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACATTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGATctct                                                  >  1:275191/1‑140 (MQ=255)                                                                                           tCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTg                                                 >  2:39735/1‑140 (MQ=255)                                                                                            cAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGt                                                >  1:464597/1‑140 (MQ=255)                                                                                                  ttGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTCCGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACg                                          >  1:19173/1‑140 (MQ=255)                                                                                                  ttGGGGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACg                                          <  1:449814/140‑1 (MQ=255)                                                                                                   tGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGc                                         >  2:507209/1‑140 (MQ=255)                                                                                                    ggTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCt                                        <  2:52141/140‑1 (MQ=255)                                                                                                     gtgtTCGACTGGGAATGGTTTGTTTTGATCTTGTTTTTAGTCTTTTATAGTAGGTTTACCACGTTCTAATTTACGTGCAGTAAAGTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCTa                                       <  1:93870/140‑1 (MQ=255)                                                                                                      tgtTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTTAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCTaa                                      <  1:534849/140‑1 (MQ=255)                                                                                                      tgtTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCCCTGTATGACGCTaa                                      <  1:306043/140‑1 (MQ=255)                                                                                                           gACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCTAAGTCaa                                 >  1:443815/1‑140 (MQ=255)                                                                                                             cTGGTAATGGTTTGTTTTGATCTTGTTCTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCAGTATGACGCTACGTCAAGa                               >  2:228790/1‑140 (MQ=255)                                                                                                              tGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCTAAGTCAAGac                              <  1:519987/140‑1 (MQ=255)                                                                                                                gTAATGGTTTGTTTTGATCTTGTTGTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCTAAGTCAAGacgt                            <  1:118214/140‑1 (MQ=255)                                                                                                                 tAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATAACGCTAAATCAAGacgta                           >  1:238385/1‑140 (MQ=255)                                                                                                                    tGGTTTGTTTTGATTGTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCTAAGTCAAGacgtaacg                        <  2:452380/140‑1 (MQ=255)                                                                                                                    tGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTACGAATGATTCAAGTTCTCTGTATGACGCTAAGTCAAAacgtaacg                        >  1:235289/1‑140 (MQ=255)                                                                                                                      gtttgtttTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCTAAGTCAAGacgtaacgta                      <  1:272451/140‑1 (MQ=255)                                                                                                                         tgtttTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCTAAGTCAAGACGTAACGTACCa                   <  2:227893/140‑1 (MQ=255)                                                                                                                         tgtttTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCTAAGTCAAGACGTAACGTACCa                   <  2:507660/140‑1 (MQ=255)                                                                                                                         tgtttTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCTAAGTCAAGACGTAACGTACCa                   <  1:521090/140‑1 (MQ=255)                                                                                                                              tGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCTAAGTCAGGACGTAACGTACCAGCAAc              >  2:171916/1‑140 (MQ=255)                                                                                                                                 tCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCTAAGTCAAGACGTAACGTACCAGCAACttt           >  2:419791/1‑140 (MQ=255)                                                                                                                                     gTTTTTAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCTAAGTCAAGACGTAACGTACCAGCGACTttgttc       >  2:18242/1‑140 (MQ=255)                                                                                                                                     gTTTTTAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCTAAGTCAAGACGTAACGTACCAGCAACTgtcttc       >  2:18235/1‑140 (MQ=255)                                                                                                                                     gTTTTTAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCTAAGTCAAGAAGTAACGTACCAGCAACTttcttc       >  2:18252/1‑140 (MQ=255)                                                                                                                                     gTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCTAAGTCAAGACGTAACGTACCAGCAACTttcttc       <  2:403744/140‑1 (MQ=255)                                                                                                                                        ttAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCTAAGTCAAGACGTAACGTACCAGCAAGTTTCTTCAtt    >  2:441568/1‑140 (MQ=255)                                                                                                                                          aaGACTTCACAAGTACCCTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCTAAGTCAAGACGTAACGTACCAGCAACTTTCTTCATTGc  >  2:120596/1‑140 (MQ=255)                                                                                                                                          |                                                                                                                                            ATTCTGCCCAGTGGTTTAACTCGTCTTCAAAACGTGTGATATCTACAACTGGAATATCATCTAAATATCCTTTTGTTAATGCATAAATAATCAACACTTGGTGTTCGACTGGTAATGGTTTGTTTTGATCTTGTTTTAAGACTTCAACAGTACGTTTACCACGTTCTAATTTACTTGCAGTAAATTCATCAAGGTCTGAACCGAATTGTGCAAATGATTCAAGTTCTCTGTATGACGCTAAGTCAAGACGTAACGTACCAGCAACTTTCTTCATTGC  >  USA300TCH1516_ALE/2223779‑2224055

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: ‑