Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,774,993 A→G 14.4% D731D (GAT→GAC)  clfB ← Clumping factor B

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,774,9930AG14.4% 149.0 / 5.1 83D731D (GAT→GAC) clfBClumping factor B
Reads supporting (aligned to +/- strand):  ref base A (39/29);  new base G (10/4);  total (49/34)
Fisher's exact test for biased strand distribution p-value = 3.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AATCCGAATCGCTATCTGAATCTGAATCGCTATCCGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTC  >  USA300TCH1516_ALE/2774854‑2775127
                                                                                                                                           |                                                                                                                                       
aaTCCGAATCGCTATCTGAATCTGAATCGCTATCCGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTa                                                                                                                                         <  1:308502/140‑1 (MQ=255)
aaTCCGAATCGCTATCTGAATCTGAATCGCTATCCGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTa                                                                                                                                         <  1:677308/140‑1 (MQ=255)
 aTCCGAATCGCTATCTGAATCTGAATCGCTATCCGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAt                                                                                                                                        >  1:68325/1‑140 (MQ=255)
 aTCCGAATCGCTATCTGAATCTGAATCGCTATCCGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGATGTTTGACAGATAGGCGCTGTTTGAGTCCCAATCGCTATCTGAATCTGAGTCGCTAt                                                                                                                                        >  1:695147/1‑140 (MQ=14)
                       gaatcGCTATCCGAGTCTGAGTCGCTGTCTGAATCTGCATCGCTGTCTAAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctga                                                                                                                  <  1:129061/140‑1 (MQ=255)
                       gaatcGCTATCCGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTGTCTGAGTCTGATGCGCTGtctgggtcggaatcgctgtctgg                                                                                                                  >  2:516065/1‑139 (MQ=14)
                       gaatcGCTATCCGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctga                                                                                                                  >  1:205034/1‑140 (MQ=255)
                         atcGCTATCCGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTGTCTGAATCTGAGTCGCTGtctgagtctgggtcgctctctgagt                                                                                                                >  2:109446/1‑140 (MQ=14)
                          tcGCTATCCGAGGCCGAGGCGCGGTCGGAGGCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtc                                                                                                               <  1:239101/140‑1 (MQ=14)
                            gCTATCCGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAATCGCTGTCTGAGTCTGAATCGCTGTGTGAATCTGTATCGATGtgtgagtctgagtcgttgtgtgagtctg                                                                                                             >  2:339510/1‑140 (MQ=14)
                             cTATCCGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGtctgggtctgactcgcttgatgagtctga                                                                                                            >  2:579993/1‑140 (MQ=14)
                             cTATCCGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtgtgg                                                                                                            >  1:174395/1‑139 (MQ=255)
                              tATCCGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCCGAAAAGCTGTTACAATCGCAATGGCTGtctgagtccgagtcgctctcggaggccggg                                                                                                           >  2:497408/1‑134 (MQ=14)
                                  cgggTCTGAGTCGTTGTCTGAGTCTGGGTGGCGGTCTGAGTCTGAGTCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtctgagtcgc                                                                                                       <  2:621327/137‑1 (MQ=11)
                                  cGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtctgagtcgc                                                                                                       <  1:571898/140‑1 (MQ=255)
                                   gAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCCATCTGAATCTGAGTCGCTAtctgagtctgagtcgctgtctgagtctgagtcgct                                                                                                      <  1:684707/140‑1 (MQ=255)
                                       cTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAGTCTGACTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTgagtctgagtcgctgtctgagtctgagtcgctgtct                                                                                                  <  2:148748/140‑1 (MQ=255)
                                              gCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGagtcgctgtctgagtctgagtcgctgtctgagtctg                                                                                           >  1:72988/1‑140 (MQ=255)
                                               cTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAATCGCTGTCTGAGTCTGAATCACTGTCTGAGTCTGAGGCGCTGTCTGAGTGTAGgtcgctgtgtgggtgggagtcgccgtctgagtctga                                                                                          >  2:245009/1‑140 (MQ=14)
                                                   ctgaatctgaatCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTGTCTGAATCTGAGTCGCTGTCTGAGTCTGCGTCGCTGTCTGAGTCGGAGTCGCTGTCTGACTCTGAGTCg                                                                                      >  2:433498/1‑140 (MQ=14)
                                                   ctgaatctgaatCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTGTCCGAATCAGAGTCGCTGACTGAGTCAGAGTCGCGGTCTGAGTCTGAGTCGAAGGCTGAAACAGAATCg                                                                                      >  2:506457/1‑140 (MQ=14)
                                                         ctgaatcGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTatct                                                                                >  1:73717/1‑140 (MQ=255)
                                                          tgaatcGCTGTCTGAGTCCGAATCGCTATCTGAGTCTGAGTCGCTGTGTGAGTCTGAATCTCGGTGTGCGTCGGAGTCGCGATGAGCGTCTGAGTCGCTGCGGGAGTCGGAGTCGCAGGCTGAGTCTCGATCGcgcgcgg                                                                               >  2:436949/1‑134 (MQ=9)
                                                          tgaatcGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTGTCTGagtctgagtcgctgtctgagtctgagtcgctgtctgagtctgagtcgctgtctgagtctgagtcgctgtctg                                                                               >  2:666055/1‑140 (MQ=11)
                                                          tgaatcGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTGTCTGAGTCTGAGGCGCTATCTGAGTCTGAGTCGGTGTGTGAGTCTGAGTCGCTGTCTGAGTCTGACTCGCTatctg                                                                               >  2:174343/1‑140 (MQ=14)
                                                          tgaatcGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTatctg                                                                               >  1:339235/1‑140 (MQ=255)
                                                               cGCTGTCTGAGTCCGAGTCGCTCGCTGAACCTGAGTCGCTGTCTGAGTCTGACTCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTatctgaatc‑t                                                                         <  2:545925/140‑1 (MQ=17)
                                                               cGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCGGAATCGGAATCGCCatctgaatc‑t                                                                         >  2:337288/1‑140 (MQ=14)
                                                                gCTGTCTGAGTCCGAAGCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTatctgaatc‑tg                                                                        <  1:546247/140‑1 (MQ=255)
                                                                 cTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGCATCGCGgtctggatc‑tgg                                                                       >  2:209337/1‑139 (MQ=11)
                                                                 cTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTgtcggagtc‑tga                                                                       >  2:95939/1‑140 (MQ=255)
                                                                  tGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTCGCAGAGTCTGAATCGCTATCTGGGTC‑TGAg                                                                      >  2:634122/1‑140 (MQ=14)
                                                                  tGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTATGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAg                                                                      >  1:371302/1‑140 (MQ=255)
                                                                    tCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAGTCTGAGTCGCTATCTGAATCTGAAGCGCTGTCTGAGTGTGATGCGCTGTCTGAGTTTGAATCGGTATGTGAATC‑TGAggt                                                                    >  2:358180/1‑138 (MQ=14)
                                                                    tCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGATTCTGAATCGCTATCTGAGTCTGTATCGGTGTCTGAGTCTGTCTCGCTgtgtgaaac‑tgccgc                                                                    >  2:103723/1‑136 (MQ=11)
                                                                    tCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCTCTATCTGACTC‑TCAGTc                                                                    >  1:362816/1‑140 (MQ=255)
                                                                    tCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTc                                                                    >  1:286819/1‑140 (MQ=255)
                                                                       gAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCt                                                                 <  1:247698/140‑1 (MQ=255)
                                                                       ctgTCTGAGTCGCTTTCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTTTCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCt                                                                 <  2:532824/138‑1 (MQ=14)
                                                                        aGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGcgg                                                                >  1:395733/1‑138 (MQ=255)
                                                                          tCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTATCTGAATC‑TGAGTCGCTgtc                                                              >  1:143708/1‑140 (MQ=255)
                                                                                   cTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTCTCTGATTC‑TGCGTCACTgtctgagtccga                                                     >  2:405726/1‑140 (MQ=14)
                                                                                   cTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTgtctgagtctga                                                     <  1:239145/140‑1 (MQ=255)
                                                                                    tATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCGGAGTCTGAGTCGCTGTCTGAGTCGGTATCGCTATCTGAATCTGAGTCGCTATCTGAGTG‑TGAGTCGCTGtctgaatcagag                                                    >  2:675153/1‑140 (MQ=11)
                                                                                     atctgaatctgaGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTctgcgtctgagt                                                   >  1:390725/1‑140 (MQ=255)
                                                                                      tctgaatctgaGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGCGCATGGCGCGATCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCtgagtctgagtc                                                  <  1:328213/140‑1 (MQ=14)
                                                                                       ctgaatctgaGTATCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGGCGCTGTCTGAGTCTGAATCGCTATTTGATTC‑TGAGTCGCTGTCTGAGtctgagtcg                                                 <  1:215860/140‑1 (MQ=17)
                                                                                        tgaatctgaGTCGCTGTCTGAGTCTGCATCGCTATCTGACTCTGAGTCGCTATCGGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGtctgagtcgc                                                <  1:625754/140‑1 (MQ=255)
                                                                                            tccgaGTCGCTATCCGAGTCTGAGTCGCTATCTGAGTCTGAATCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTGTCTGAATC‑AGAGTCGCTGTGTGAGactgagtcgcgggc                                            >  2:552157/4‑136 (MQ=11)
                                                                                                aGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGtctgagtcgctgtctgaa                                        >  1:657106/1‑140 (MQ=255)
                                                                                                aGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCGAACGCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGtctgagtcgctgtctgaa                                        >  1:481577/1‑140 (MQ=255)
                                                                                                aGTCGCTGTCTGAGTCTGAATCGATATCTGAATGGGAGTCGCTATCTGAGTCTGAGTCGGTGTCTGAGTCTGAGTGGGTCTCTGAGTCTGAGTCGCTATCTGAGGC‑GGACTCGCCATCTGAGtcagaagcgctatcggaa                                        >  2:503575/1‑140 (MQ=2)
                                                                                                aGTCGCTGTCCGTGTCCGAGTCGCTTTCTGAATCTGAGTCGCTATCTGAGTCCGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTATCTGAATC‑TGAGTCGCTGTCTGAGtctgagtcgctgtctgaa                                        <  2:635531/140‑1 (MQ=14)
                                                                                                aGTCGCTCTCTGAGTCTGAGTCGCTCTCCGAGTCTGACTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTATCTGAGTCTGAGTCGCTATCTGAgtc‑tgagtcgctgtctgagtctgagtcgctgtctgag                                        <  2:437248/140‑2 (MQ=1)
                                                                                                 ctCGCTGTCTCGGTCTGATTCGCTATCTGCATCTGAGTCGCTGTCTGAGTCTGATTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGtctgagtcgctgtctgaat                                       <  2:17152/139‑1 (MQ=14)
                                                                                                  tggCTGTCTGGGTCTGAGTCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGtctgagtcgctgtctgaatc                                      <  1:288273/138‑1 (MQ=255)
                                                                                                  tCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGCGTAGCTCTCTGAAtctgaatagatcgctgaatc                                      >  2:373071/1‑140 (MQ=14)
                                                                                                    gCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTGTCTGATTC‑TGAGTCGCTGTCTGCAtctgactcgctgtccgactctg                                    >  2:327487/1‑140 (MQ=14)
                                                                                                            tgtgtgaTTCTCTATTTGATTCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGtctgagtcgctgtctgaatctgagtcgctg                            <  2:386032/136‑1 (MQ=14)
                                                                                                             gtctgaATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGtctgagtcgctgtctgaatctgagtcgctgt                           <  1:498735/140‑1 (MQ=255)
                                                                                                             ggctgtctCGCTGTCTTAATCGGACTCCCTGTCTGAGTCTGAGCCGCTGTCTGAGTCGGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGtctgagtcgctgtctgaatctgagtcgctgt                           <  2:460109/133‑1 (MQ=14)
                                                                                                                tgaATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGtctgagtcgctgtctgaatctgagtcgctgtctg                        >  1:367522/1‑140 (MQ=255)
                                                                                                                  agtCGCTCTCGGACTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGtctgagtcgctgtctgaatctgagtcgctgtctgaa                      <  2:542616/138‑1 (MQ=14)
                                                                                                                   aTCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAAGCTGACTCGGTATCTGAATC‑TGACGCGCTATCTGAGTctgagtcgctatctaagtacgattcgctgtctgcat                     >  2:530197/1‑140 (MQ=11)
                                                                                                                   aTCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTCTCTGAGTCTGAACCGCTATCCCACTCAAGAGCAACTAGGT‑AGTgtgagacgctgtcggaatccgagtcgctggccgaat                     >  2:313315/1‑140 (MQ=2)
                                                                                                                   aTCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGACGCTGTCTGGGTCTGAATCACTGTCTGAGTG‑TGAGTCGCTGTCTGAGTctgagtcgctgtctgaacgtgagtcgccgtctggat                     >  2:535048/1‑140 (MQ=14)
                                                                                                                     cGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGACTCTGAGTCGCTGTCTGAGTCTTACTCGCTGTCTGACTC‑TGCGCCGCTGTCTGAGTCTgcgtcgctctctggacccgcatcgctgtctaactct                   >  1:47735/1‑140 (MQ=14)
                                                                                                                      gctatctgagtctgagtcgctatctgagtctgagtcGCTGTCTGAGTCTGCGTCGCTGTCTGAGCCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGTCTGagtcgctgtctgaatctgagtcgctgtctgaatctg                  <  1:549754/140‑1 (MQ=255)
                                                                                                                      gCTATCTGCGGCTGAGTCGCTTTCTGAGTCTGAGTCGCTGTCTGAGTCTGGCTCGCTGTCCGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGTCTGagtcgctgtctgaatctgagtcgctgtctgaatctg                  <  2:646908/140‑1 (MQ=14)
                                                                                                                      gCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGGTATCTGACTC‑GGAGGCGGTGTCGGCATCtgagacgatgtctgaatcggagtcggcgtcggaatcgg                  >  2:664287/1‑138 (MQ=14)
                                                                                                                      gCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGCATC‑TGAGTCGCTGTCTGAGTCTGagtcgctgtctgaatctgagtcgctgtctgaatctg                  <  1:629949/140‑1 (MQ=255)
                                                                                                                      gCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGTCTGagtcgctgtctgaatctgagtcgctgtctgaatctg                  <  1:702920/140‑1 (MQ=255)
                                                                                                                      gCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGTCTGagtcgctgtctgaatctgagtcgctgtctgaatctg                  <  1:433477/140‑1 (MQ=255)
                                                                                                                      gCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGTCTGagtcgctgtctgaatctgagtcgctgtctgaatctg                  <  1:164030/140‑1 (MQ=255)
                                                                                                                       cTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGTCTGAgtcgctgtctgcatctgggtcgctgtctgagtctga                 >  1:425877/1‑140 (MQ=255)
                                                                                                                       cTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAATCGCTGTCTGAGTCTGAcgcgctgtctgaatctgaatcgctgtctgactcaga                 >  2:60577/1‑140 (MQ=14)
                                                                                                                            tgaatctgaGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGc            <  1:145486/140‑1 (MQ=255)
                                                                                                                             gactctgcGTCGCTAGGTGAGTCTGAGTCGTTGTGCGAGCCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAGTC‑TGAGTGGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTTTGAATCTGAATCGCt           <  1:302292/137‑1 (MQ=14)
                                                                                                                                tctgaGTCGCTAtctgagtctgagtcgctgtctgagtctg                                                                                                             <  1:602162/40‑1 (MQ=255)
                                                                                                                                tctgaGTCGCTAtctgagtctgagtcgctgtctgagtctg                                                                                                             <  1:140301/40‑1 (MQ=255)
                                                                                                                                 ctgaGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTgtct       >  1:660347/1‑140 (MQ=255)
                                                                                                                                 ctgaGCCGCCATCCGAGTCTGAGCCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTgtct       <  1:445442/140‑1 (MQ=255)
                                                                                                                                   gaGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGTGTTTGAGTCGCTATCTAATTA‑TGAGTCGCTGTCTTAGTCTGATTCGCTTTCTGAATTTTAGTTACTCGTTGATTCTGAATGGATgtctga     >  1:630112/1‑140 (MQ=9)
                                                                                                                                    aGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAATCTGACTCGCGgtctgag    >  2:194273/1‑140 (MQ=255)
                                                                                                                                      tCGCTGTCTGAGTCTGAGTCGCAGTCTGAGTCGGAGGCGCCGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTgtctgagtc  <  1:300541/140‑1 (MQ=17)
                                                                                                                                      tCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAGTC‑TGAGTCGCTGTCTGAGTCTGAGTCGGTGTCTGAATCTGAGTCGCTGTGTGCATCTGAATCGCTgactgagtc  >  2:325901/1‑140 (MQ=17)
                                                                                                                                      tCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTgtctgagtc  <  1:289482/140‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                       
AATCCGAATCGCTATCTGAATCTGAATCGCTATCCGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATC‑TGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTC  >  USA300TCH1516_ALE/2774854‑2775127

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑