Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,448,484 A→G 12.5% intergenic (‑243/+34) yxeP_4 ← / ← hutI putative hydrolase YxeP/Imidazolonepropionase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,448,4840AG12.5% 271.8 / 23.7 96intergenic (‑243/+34)yxeP_4/hutIputative hydrolase YxeP/Imidazolonepropionase
Reads supporting (aligned to +/- strand):  ref base A (34/50);  new base G (2/10);  total (36/60)
Fisher's exact test for biased strand distribution p-value = 2.01e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACTATTCTAACTTTTATAATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCTTACCGTCTTTAATAACTTT  >  USA300TCH1516_ALE/2448394‑2448574
                                                                                          |                                                                                          
aaCTATTCTAACTTTTATAATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTa                                                                                            <  1:330043/91‑1 (MQ=255)
 aCTATTCTAACTTTTATAATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAg                                                                                           >  1:1893447/1‑91 (MQ=255)
 aCTATTCTAACTTTTATAATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAg                                                                                           <  1:3870024/91‑1 (MQ=255)
  cTATTCTAACTTTTATAATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGt                                                                                          <  1:2575669/91‑1 (MQ=255)
   tATTCTAACTTTTATAATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGtt                                                                                         <  1:805868/91‑1 (MQ=255)
    aTTCTAACTTTTATAATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGttt                                                                                        <  1:617806/91‑1 (MQ=255)
     ttCTAACTTTTATAATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTa                                                                                       >  1:865017/1‑91 (MQ=255)
      tCTAACTTTTATAATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTaa                                                                                      <  1:3278992/91‑1 (MQ=255)
      tCTAACTTTTATAATTGAGACTCTATACAAAAACGTGTTCTCGAATACACTTGTTTTTACAAACCACAAAAAGCTCTCAACATTAGTTTaa                                                                                      >  1:4150220/1‑91 (MQ=255)
        tAACTTTTATAATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAAc                                                                                    <  1:473579/91‑1 (MQ=255)
         aaCTTTTATAATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAAcc                                                                                   <  1:1810517/91‑1 (MQ=255)
            ttttATAATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACGAAt                                                                                >  1:3221442/1‑91 (MQ=255)
             tttATAATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAGCATTGGTTTAAACTAATg                                                                               <  1:1482702/91‑1 (MQ=38)
              ttATAATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGc                                                                              <  1:3518641/91‑1 (MQ=255)
               tataATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCt                                                                             <  1:3529960/91‑1 (MQ=255)
                 taATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAGCATTGGTTTAAACTAATGTTTa                                                                           <  1:4071634/91‑1 (MQ=37)
                 taATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAGCATTGGTTTAAACTAATGTTTa                                                                           <  1:477610/91‑1 (MQ=37)
                 taATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTa                                                                           >  1:1036263/1‑91 (MQ=255)
                 taATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTa                                                                           >  1:3935171/1‑91 (MQ=255)
                 taATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTa                                                                           >  1:2803679/1‑91 (MQ=255)
                  aaTTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAGCATTGGTTTAAACTAATGTTTag                                                                          <  1:3369291/91‑1 (MQ=37)
                  aaTTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAGCATTGGTTTAAACTAATGTTTag                                                                          <  1:370575/91‑1 (MQ=37)
                  aaTTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAGCATTGGTTTAAACTAATGTTTag                                                                          <  1:1294213/91‑1 (MQ=37)
                   aTTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAGCATTGGTTTAAACTAATGTTTaga                                                                         <  1:302313/91‑1 (MQ=25)
                   aTTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAGCATTGGTTTAAACTAATGTTTaga                                                                         <  1:2264926/91‑1 (MQ=37)
                   aTTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAGCATTGGTTTAAACTAATGTTTaga                                                                         <  1:764392/91‑1 (MQ=25)
                   aTTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTaga                                                                         <  1:608709/91‑1 (MQ=255)
                   aTTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTaga                                                                         >  1:898216/1‑91 (MQ=255)
                   aTTGAGACTCGATACAAAACCGTGTTCTCGAATATACTTGTTTTTACACACCACAAAAAGCGCTAAACATTAGTTTAAACCAATGCTTaga                                                                         <  1:919677/91‑1 (MQ=255)
                    ttGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAATGCTCTAAGCATTGGTTTAAACTAATGTTTagag                                                                        <  1:2730030/91‑1 (MQ=25)
                        gaCTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCttt                                                                    <  1:2960296/91‑1 (MQ=255)
                        gaCTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCttt                                                                    <  1:3472157/91‑1 (MQ=255)
                          ctctATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCt                                                                  <  1:3190787/91‑1 (MQ=255)
                           tctATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTa                                                                 >  1:1251458/1‑91 (MQ=255)
                           tctATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTa                                                                 <  1:3938538/91‑1 (MQ=255)
                              ataCAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAatt                                                              <  1:675605/91‑1 (MQ=255)
                              ataCAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAatt                                                              <  1:675373/91‑1 (MQ=255)
                                 cAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAattatt                                                           <  1:3921431/91‑1 (MQ=255)
                                  aaaaaCGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTAttt                                                          <  1:2582482/91‑1 (MQ=255)
                                   aaaaCGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTAtttt                                                         <  1:2657963/91‑1 (MQ=255)
                                   aaaaCGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTAtttt                                                         >  1:1949173/1‑91 (MQ=255)
                                   aaaaCGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTAtttt                                                         <  1:2658412/91‑1 (MQ=255)
                                    aaaCGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTa                                                        >  1:2135274/1‑91 (MQ=255)
                                    aaaCGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTa                                                        <  1:3062026/91‑1 (MQ=255)
                                     aaCGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTAt                                                       <  1:2798421/91‑1 (MQ=255)
                                     aaCGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTAt                                                       <  1:2798388/91‑1 (MQ=255)
                                     aaCGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTAt                                                       <  1:2798162/91‑1 (MQ=255)
                                     aaCGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTCTAt                                                       >  1:1546249/1‑91 (MQ=255)
                                       cGTGTTCTCGAATATACTTGTTTTTACAAACCAGAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGc                                                     <  1:3688400/91‑1 (MQ=255)
                                         tgtTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTACACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCtt                                                   <  1:4136069/91‑1 (MQ=255)
                                         tgtTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCtt                                                   >  1:3649127/1‑91 (MQ=255)
                                         tgtTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCtt                                                   >  1:3081435/1‑91 (MQ=255)
                                          gtTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCttt                                                  >  1:129566/1‑91 (MQ=255)
                                          gtTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCttt                                                  >  1:1427765/1‑91 (MQ=255)
                                           ttCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTa                                                 <  1:2008809/91‑1 (MQ=255)
                                              tcGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTaaaa                                              <  1:913764/91‑1 (MQ=255)
                                                  atatACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATa                                          <  1:2058753/91‑1 (MQ=255)
                                                   tataCTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATAc                                         <  1:4130898/91‑1 (MQ=255)
                                                   tataCTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATAc                                         <  1:4127662/91‑1 (MQ=255)
                                                   tataCTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATAc                                         <  1:4125350/91‑1 (MQ=255)
                                                   tataCTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATAc                                         <  1:4125349/91‑1 (MQ=255)
                                                     taCTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACtg                                       >  1:2268542/1‑91 (MQ=255)
                                                      aCTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACtgt                                      >  1:1373780/1‑91 (MQ=255)
                                                      aCTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACtgt                                      <  1:272782/91‑1 (MQ=255)
                                                        ttGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTgtgt                                    <  1:3607402/91‑1 (MQ=255)
                                                        ttGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTgtgt                                    <  1:3607728/91‑1 (MQ=255)
                                                        ttGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTgtgt                                    >  1:1869978/1‑91 (MQ=255)
                                                          gTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTa                                  <  1:2323352/91‑1 (MQ=255)
                                                            ttttACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATc                                >  1:3894146/1‑91 (MQ=255)
                                                            ttttACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATc                                <  1:4083305/91‑1 (MQ=255)
                                                              ttACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTa                              <  1:3000923/91‑1 (MQ=255)
                                                               tACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTAc                             >  1:3361898/1‑91 (MQ=255)
                                                                aCAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACg                            <  1:2241498/91‑1 (MQ=255)
                                                                 cAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGa                           >  1:1209507/1‑91 (MQ=255)
                                                                 cAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGa                           >  1:806968/1‑91 (MQ=255)
                                                                 cAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGa                           >  1:806800/1‑91 (MQ=255)
                                                                 cAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGa                           >  1:2436434/1‑91 (MQ=255)
                                                                   aaCCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATg                         <  1:1532220/91‑1 (MQ=255)
                                                                    aCCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGa                        <  1:2852609/91‑1 (MQ=255)
                                                                      cacaAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGAcc                      >  1:2977293/1‑91 (MQ=255)
                                                                       acaAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCt                     >  1:3727251/1‑91 (MQ=255)
                                                                       acaAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCt                     <  1:123564/91‑1 (MQ=255)
                                                                        caAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCtt                    >  1:2590411/1‑91 (MQ=255)
                                                                        caAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCtt                    >  1:2590655/1‑91 (MQ=255)
                                                                        caAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCtt                    >  1:1730793/1‑91 (MQ=255)
                                                                        caAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCGAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCtt                    <  1:3308558/91‑1 (MQ=255)
                                                                        caAAAAGCTCTAAACATTAGTTTAAACCAATGCATAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCtt                    <  1:3676263/91‑1 (MQ=255)
                                                                           aaaGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCTTAcc                 <  1:1988953/91‑1 (MQ=255)
                                                                           aaaGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCTTAcc                 >  1:1519712/1‑91 (MQ=255)
                                                                            aaGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCTTACCg                >  1:825043/1‑91 (MQ=255)
                                                                               ctctAAGCATTGGTTTAAACTAATGTTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCTTACCGTCt             >  1:2860067/1‑91 (MQ=25)
                                                                                 ctAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCTTACCGTCttt           >  1:760093/1‑91 (MQ=255)
                                                                                  tAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCTTACCGTCTTta          >  1:2040234/1‑91 (MQ=255)
                                                                                   aagcATTGGTTTAAACTAATGTTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCTTACCGTCTTtaa         >  1:3749561/4‑91 (MQ=37)
                                                                                   aaaCATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCCTACCGTCTTtaa         <  1:3180229/91‑1 (MQ=255)
                                                                                       aTTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCTTACTGTCTTTAATAAc     <  1:3202807/91‑1 (MQ=255)
                                                                                        ttAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCTTACCGTCTTTAATAACt    <  1:1917210/91‑1 (MQ=255)
                                                                                          aGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCTTACCGTCTTTAATAACttt  >  1:2527080/1‑91 (MQ=255)
                                                                                          aGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCTTACCGTCTTTAATAACttt  >  1:2525584/1‑91 (MQ=255)
                                                                                          |                                                                                          
AACTATTCTAACTTTTATAATTGAGACTCTATACAAAAACGTGTTCTCGAATATACTTGTTTTTACAAACCACAAAAAGCTCTAAACATTAGTTTAAACCAATGCTTAGAGCTTTCTAATTATTTTATGCTTTAAAAGATACTGTGTTATCTACGATGACCTTACCGTCTTTAATAACTTT  >  USA300TCH1516_ALE/2448394‑2448574

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑