Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,857,839 T→C 7.0% I179V (ATT→GTT)  USA300HOU_RS09235 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,857,8390TC 7.0% 184.3 / 3.0 76I179V (ATT→GTT) USA300HOU_RS09235hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (35/35);  new base C (2/4);  total (37/39)
Fisher's exact test for biased strand distribution p-value = 6.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTT  >  USA300TCH1516_ALE/1857702‑1857979
                                                                                                                                         |                                                                                                                                             
atCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATTCCACTGCTTTTGGTTCTTCATTTGTTATAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAAtctc                                                                                                                                            <  2:342540/141‑1 (MQ=255)
atCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAAtctc                                                                                                                                            <  1:341542/141‑1 (MQ=255)
atCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAAtctc                                                                                                                                            <  1:341517/141‑1 (MQ=255)
 tCACTTTATTTTTTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGTTACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATctct                                                                                                                                           <  2:442418/141‑1 (MQ=255)
   ccTTTAATTTTTTGCACTTGCTTCTTTTTTTATCGGTGCTTGTTGTGCTTTCACTGCCACTGCTTTTGGTTTTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTtg                                                                                                                                         <  2:174994/140‑1 (MQ=17)
   aCTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCttt                                                                                                                                         >  1:740103/1‑140 (MQ=255)
     ttAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTtgtg                                                                                                                                       <  1:40002/141‑1 (MQ=255)
       aaaTTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGcc                                                                                                                                     <  1:47849/141‑1 (MQ=255)
         attattTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGccgc                                                                                                                                   >  2:402917/1‑139 (MQ=255)
         attattTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCctt                                                                                                                                   >  2:28670/1‑140 (MQ=255)
          ttttttGCACTTGCTTCTTTTTTCATCTTTGCTTGTGGTGCTGTGAAGTAGTCTGCTTTTGCTTCTTCATTTCTTCCAGCAGCACTTTTACCTGTTTCTGTTTGTGCTTCTTTTTTAGCTTCTTGAACCTCTTGTGCctat                                                                                                                                  <  2:302442/138‑3 (MQ=16)
          ttattTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCGCGGGTTACAGCCGCAACATGTTGTCTTTCGGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCctct                                                                                                                                  <  1:180909/141‑1 (MQ=14)
          ttattTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGCTTCTGCTTGTTCGTATTTTTTACCTTTTTGAATCTCTtgtgtcggt                                                                                                                                  >  2:74664/1‑136 (MQ=14)
           tattTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGTATCTCTTGTGCCTCtt                                                                                                                                 <  1:457082/141‑1 (MQ=255)
           tattTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCCTTTGGTTCTTCTTTTGATACAGCTGCACTTCTAACTGGTTCTGCTTGTGCTTCTTTTTTATCTTCTTGAGTCTCTTGTGCCTCtt                                                                                                                                 >  2:46940/1‑141 (MQ=14)
             tttGCACTTGCTTCTTCTTTTATCGCTGCTTTTTGTGCTTTTAATGCTACTGCTTTTGGTTCTTCATTTGTTACAGCTGCACTTTTGTCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTtgt                                                                                                                               <  2:32096/141‑1 (MQ=17)
              ttGCACTTGCTTCTTCTTTTGTCGCTGCTTGTTGTGCTTTCAATACCACTGCTTTTGGGTCTTTATTTGATACAGCTGCACTTTTTTCTGTTTCTGCTTGTGCTTCATTTTTAGATTCTTGAATCACTTGTGCCTCTtgtt                                                                                                                              >  1:465825/1‑140 (MQ=14)
                 cccTTTCTTCTTCTTTTCTCTCTGCTTGTTGTGCTTTCACTTCCACTTCTTTTGGTTCTTCATTTTATACAGCTGCACTTTTGTCTTTTTCTGCTTGTTCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATg                                                                                                                           <  2:276994/139‑1 (MQ=17)
                          ttttttttACCGCTGCTTGTTGTGCTTTCAATGCCACTGTTTTTGGTTCTTCATTTTTTATAGCTGCACTTTTATCTTTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCa                                                                                                                  <  2:378800/137‑1 (MQ=17)
                          cttcttTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTTTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCa                                                                                                                  <  2:63017/141‑1 (MQ=255)
                          cttcttTTATCGCTGCTTGTTGTGCTATCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCAGCTTGAGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGTCTCTTGTGATGTATCACTCa                                                                                                                  <  1:468061/141‑1 (MQ=255)
                            tcttTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCaaa                                                                                                                <  1:630128/141‑1 (MQ=255)
                                 tATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAattatt                                                                                                           >  1:435498/1‑141 (MQ=255)
                                 tATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCGTATGATGTttcattcaggttagt                                                                                                           >  2:178234/1‑134 (MQ=17)
                                       tgctTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACt                                                                                                     <  1:146107/141‑1 (MQ=255)
                                         tttgttgTGCCTTCAATGCCCCTGCTTTTGGTTCTTCATTTGATTCTGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTCAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTg                                                                                                   <  2:492310/140‑1 (MQ=25)
                                           tgttgtGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCTTCTTGTGATGTATCACTCAAATTATTTGCACTTGct                                                                                                 >  2:295273/1‑141 (MQ=255)
                                                tgCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGcttcttc                                                                                            <  1:370140/141‑1 (MQ=255)
                                                  ttttCAGTGCCACTGTTTTTGGTTTTGCATTTGTTTGTGCTGCGCTTTTGTCTTTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGcttcttc‑tt                                                                                         <  2:137864/140‑1 (MQ=17)
                                                     tCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTTCTTTTTC‑TTTTa                                                                                      >  2:523532/1‑141 (MQ=255)
                                                     tCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑ttttt                                                                                      >  2:313379/1‑140 (MQ=255)
                                                     tCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTa                                                                                      >  1:376700/1‑141 (MQ=255)
                                                      cAATGCCGCTGCTTTTGGTTATTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACATGCTTCTTC‑TTTTAt                                                                                     >  1:480277/1‑141 (MQ=255)
                                                      cAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTAt                                                                                     >  1:424260/1‑141 (MQ=255)
                                                        aTGCCACTGCTTTTGGTTCTTCATTTGCTACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAACTTATTTGCACTTGCTTCTTC‑TTTTATCg                                                                                   <  1:301045/141‑1 (MQ=255)
                                                        aTGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCg                                                                                   >  1:55661/1‑141 (MQ=255)
                                                            cACTGCTTTTGGTTCTTCATTTGATATGACTTCTCGTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCgctgc                                                                               >  1:372262/1‑141 (MQ=17)
                                                                tcTTTTGCTTCTTCATCTTTTGTTGATGCATTTTTATCTTTCTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCttgt                                                                           <  2:372807/140‑1 (MQ=14)
                                                                    ttGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTtgtg                                                                       >  1:314932/1‑141 (MQ=255)
                                                                        ttcttcATTTGGTACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTTAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCttt                                                                   <  2:625659/141‑1 (MQ=255)
                                                                                  gATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGTTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGATTTTAAttctcct                                                         >  2:108757/1‑135 (MQ=17)
                                                                                  gATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGCATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGcccag                                                         >  2:108771/1‑138 (MQ=255)
                                                                                  gATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACt                                                         >  1:236271/1‑141 (MQ=255)
                                                                                     aCAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTCATCGCTGCTTGCTGTGCCTTCAATGCCCCtccc                                                      >  2:508689/1‑138 (MQ=17)
                                                                                     aCAGCTGCACTTTTATCTGTCTCTGCTTGTGCTTCTTTTTTAGCATCTTGAATCTCTTGTGCCTCTTGTGATTTATGAATCTACGCACTTGCACTTGCCTCTTC‑TTTCATCGCTATTTGTTGTGCTTTCGATTCCAGTGCt                                                      >  2:421899/1‑141 (MQ=14)
                                                                                       aGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGAttt                                                    >  1:300029/1‑141 (MQ=255)
                                                                                        gctgtgcTTTTGTCTCTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGCATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCtttt                                                   <  1:348173/135‑1 (MQ=14)
                                                                                        gCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCtttt                                                   >  1:759692/1‑141 (MQ=255)
                                                                                        gCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCtttt                                                   <  1:591257/141‑1 (MQ=255)
                                                                                        gCTGCACTATTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCtttt                                                   <  1:348228/141‑1 (MQ=255)
                                                                                          tgtgcTTTTGTCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTTTTGTATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGa                                                 <  1:204110/137‑1 (MQ=255)
                                                                                           tcatttttGTCTTTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTTAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGAt                                                <  2:158557/137‑1 (MQ=255)
                                                                                                tttATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCTTCTTGTGATGTATCACTTAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCttgt                                                                           <  2:358549/109‑1 (MQ=12)
                                                                                                tttATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCttgt                                                                           >  1:358549/1‑109 (MQ=255)
                                                                                                tttATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCttt                                           <  1:647950/141‑1 (MQ=255)
                                                                                                  tATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCGTCTTGTGATGTATCACTCAAATTCTTTGCACTTGCTTCTTC‑TTTTGTCGCTGCTTGTTGTGCTTTTAATGCCACTGGTTTTGTttttttct                                         >  1:233385/1‑139 (MQ=14)
                                                                                                   ttCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTAtt                                        <  1:708994/140‑1 (MQ=255)
                                                                                                     ctttttCTGCTTGTGCTTCTTTTTTAGCTTCTTGAACCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTGTGATTCTTTATTTg                                      <  1:411408/138‑1 (MQ=255)
                                                                                                        tttCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCACTGCCACTGCTTTTGATTCTTTATTTGATa                                   >  1:263472/1‑141 (MQ=255)
                                                                                                          tCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACa                                 <  1:450546/141‑1 (MQ=255)
                                                                                                          tCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTCTATTTGATACa                                 <  1:633027/141‑1 (MQ=255)
                                                                                                           ttGCTTGTGCTTCTTTTTTTGCTTCTTGATTCTCTTGTGCCTCTTTTTATGTATCTCTTAAATTATTTGCACTTGCTTCTTC‑TTTTATCTCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTTATACAg                                <  2:253775/140‑1 (MQ=11)
                                                                                                            tGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGc                               >  1:391263/1‑141 (MQ=255)
                                                                                                               ttGTGCTTCTTTTTTAGCTTCTTGAACCTCTTGTGCCTCTTGTGATGTATCACTTAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCcac                            >  1:244983/1‑141 (MQ=21)
                                                                                                                tgtgCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGcttcttc                                                                                            >  1:257006/1‑77 (MQ=255)
                                                                                                                tgtgCTTCTTTTTTAGCATCTTGAATCTCTTGTGCCTCTTGTGATAACTCACTCAAAATATTTGCACTTGCTTCTTC‑TGTTATCGCTGCTTGTTGTGCCTTCATTGCCTCTGCTTTTGATTATTTATTTGATACAGcaccc                           >  2:129261/1‑137 (MQ=11)
                                                                                                                       tttttttAGCTTCTTGATCCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTAt                    <  2:244983/140‑1 (MQ=255)
                                                                                                                        tttttgAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATc                   <  1:74664/141‑1 (MQ=255)
                                                                                                                           tttAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTGCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGc                >  2:614076/1‑141 (MQ=255)
                                                                                                                           tttAGCTTCTTGAACCTCTTGTGCCTCTTGTGATGTATCACTTAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGAt                                    >  2:254875/1‑121 (MQ=2)
                                                                                                                           tttAGCTTCTTGAACCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGAt                                    <  1:254875/121‑1 (MQ=255)
                                                                                                                            ttaatttcttGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCt               <  2:305099/136‑1 (MQ=255)
                                                                                                                            ttAGCTTCTTGACTCTCTTGTGCCTTTTGTGATGTATCACTCTAATTATTTGCACTTGCTTTTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCt               <  2:300019/141‑1 (MQ=255)
                                                                                                                            ttAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCt               >  1:291891/1‑141 (MQ=255)
                                                                                                                              aGCTTCTTGAATCTCTTGTGCCGCTTGGTATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTTTTTCTTTTTTTGATGAAGCTCCCCTTTTTTCTGCttt             >  2:426951/1‑140 (MQ=14)
                                                                                                                                    ttGAATCTTTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTTTTCTTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCtt        <  2:397588/141‑1 (MQ=255)
                                                                                                                                       aaTCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCCTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGc    <  1:105344/141‑1 (MQ=255)
                                                                                                                                        aTCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTTTTTTTTTATTTTATACAGCCACACTTTTACCTGCTTTTGCTTGTGCt   >  2:696072/1‑141 (MQ=14)
                                                                                                                                        aTCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCGTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCt   >  1:304267/1‑141 (MQ=255)
                                                                                                                                         tctcTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCAGCTTCTGCTTGTGCtt  >  1:416772/1‑141 (MQ=255)
                                                                                                                                         tctcTTGTGCCTATTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCtt  >  1:542028/1‑141 (MQ=255)
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ATCACTTAAATTATTTGCACTTGCTTCTTCTTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGGTTCTTCATTTGATACAGCTGCACTTTTATCTGTTTCTGCTTGTGCTTCTTTTTTAGCTTCTTGAATCTCTTGTGCCTCTTGTGATGTATCACTCAAATTATTTGCACTTGCTTCTTC‑TTTTATCGCTGCTTGTTGTGCTTTCAATGCCACTGCTTTTGATTCTTTATTTGATACAGCCACACTTTTATCCGCTTCTGCTTGTGCTT  >  USA300TCH1516_ALE/1857702‑1857979

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: ‑