Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A1 F41 I0 R1 38 250.3 5754022 94.2% 5420288 134.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,532,298 A→T 100% T15T (ACA→ACT)  femA_3 → Aminoacyltransferase FemA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,532,2980AT100.0% 691.8 / ‑6.5 227T15T (ACA→ACT) femA_3Aminoacyltransferase FemA
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (87/138);  minor base G (0/2);  total (87/140)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

Only 100 of 228 total aligned reads displayed.

TTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGAC  >  USA300TCH1516_ALE/2532167‑2532426
                                                                                                                                   |                                                                                                                                 
   gTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACaaa                                                                                                                              >  2:1318900/1‑134 (MQ=255)
   gTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTGACTACaaa                                                                                                                              >  2:811852/1‑134 (MQ=255)
   gTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGAGTTTAATACaaa                                                                                                                              >  1:2768986/1‑134 (MQ=255)
    tAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTTAATAATTATAGTTCAATTCAGTGATGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAg                                                                                                                             <  1:263368/134‑1 (MQ=255)
    tAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAg                                                                                                                             <  1:515950/134‑1 (MQ=255)
      aTCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCa                                                                                                                           <  2:2289938/134‑1 (MQ=255)
       tCAGTTTTTGATAAAATAAACAAAGAGCAGTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAt                                                                                                                          <  2:1877561/134‑1 (MQ=255)
       tCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCTGAGAGGGATCCGATATACTGGCCATCAGTACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAt                                                                                                                          <  2:2048225/134‑1 (MQ=255)
        cAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGAATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAACAtt                                                                                                                         >  1:1645821/1‑134 (MQ=255)
            ttttGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTc                                                                                                                     >  1:226389/1‑134 (MQ=255)
            ttttGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTAAATACAGAGAGGGATGGGATAAACTGAATTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTAGTACAAAGCATTTTTc                                                                                                                     >  2:1170997/1‑134 (MQ=255)
             tttGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGATGGATTGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTc‑a                                                                                                                   <  1:2406088/134‑1 (MQ=255)
             tttGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGTATATAATGAATTTTGTAACGTTGACTGCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTc‑a                                                                                                                   <  1:635/134‑1 (MQ=255)
                gATAAAATAAAAAAATAGCATTATTAATATATTCAAAAATTATAGTTCAATTCAGTTAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACAt                                                                                                                <  1:1240575/134‑1 (MQ=255)
                gATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTA‑ACAt                                                                                                                <  2:2101355/134‑1 (MQ=255)
                         aaaaaaTAGCATAATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATCAGATTGCTACAAAGCATATTTC‑ACATTACACACaa                                                                                                       >  2:2737106/1‑134 (MQ=255)
                          aaaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAAt                                                                                                      >  1:177036/1‑134 (MQ=255)
                          aaaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAAt                                                                                                      <  1:2237776/134‑1 (MQ=255)
                          aaaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACATTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAAt                                                                                                      >  1:847087/1‑134 (MQ=255)
                              aTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGc                                                                                                  <  2:168478/134‑1 (MQ=255)
                                   attattAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTc                                                                                             <  1:1673036/134‑1 (MQ=255)
                                   attattAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTc                                                                                             <  2:968842/134‑1 (MQ=255)
                                      attaATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCAtt                                                                                          <  2:1265854/134‑1 (MQ=255)
                                        tgataaATTCAAGAATTATAGTTCAATTCAGAGAAGGATGGGATAAAATGAACTTTTTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTAc                                                                                        <  2:658994/132‑1 (MQ=255)
                                         aataaATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACa                                                                                       <  2:1060740/134‑1 (MQ=255)
                                          ataaATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACaa                                                                                      >  1:2611174/1‑134 (MQ=255)
                                           taaATTCATAAATTATAGTTTAATTCATAGATGGATTGGATAAAATGAATTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAAt                                                                                     <  1:478018/134‑1 (MQ=255)
                                           taaATTCAAAAATTATAGTTTAATTAATAGAGGGATGGGGTACTACAAACGTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAAt                                                                                     <  1:2837588/134‑1 (MQ=255)
                                             aaTTCAAAAATTATAGTTCAATTCAGAGAGGGATGTGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCa                                                                                   <  1:2727134/134‑1 (MQ=255)
                                              aTTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCAt                                                                                  <  2:2601529/134‑1 (MQ=255)
                                              aTTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCAt                                                                                  <  2:2790232/134‑1 (MQ=255)
                                               ttCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTTTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATa                                                                                 <  1:2550252/134‑1 (MQ=255)
                                                tCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGTGTTTAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATag                                                                                <  1:41504/134‑1 (MQ=255)
                                                tCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCATTTCTTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATag                                                                                >  1:2105084/1‑134 (MQ=255)
                                                   aaaaTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGt                                                                             >  2:919617/1‑134 (MQ=255)
                                                   aaaaTTATAGTTCAATTCAGAGAGGGATGCGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGt                                                                             >  2:1598023/1‑134 (MQ=255)
                                                   aaaaTTATAGTTCAAAACAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGt                                                                             >  2:2710013/1‑134 (MQ=255)
                                                      aTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGa                                                                          <  2:1222667/134‑1 (MQ=255)
                                                        tataGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGAtt                                                                        <  1:947068/134‑1 (MQ=255)
                                                         ataGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGAttt                                                                       >  2:2433917/1‑134 (MQ=255)
                                                            gTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTTCAGGGGACAACAGACGAGTAATATTTTTTTGGTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTaaa                                                                    <  1:396211/134‑1 (MQ=255)
                                                                 aTTCAGAGAGGGATGGGATAAATTGAACTTTATAACTTTGACTTCGGATTAGTTCAATTCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCg                                                               <  1:2150836/134‑1 (MQ=255)
                                                                 aTTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCg                                                               <  2:1431940/134‑1 (MQ=255)
                                                                 aTTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCg                                                               <  1:1379211/134‑1 (MQ=255)
                                                                  ttCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGa                                                              >  2:1295532/1‑134 (MQ=255)
                                                                  ttCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGa                                                              >  1:1817357/1‑134 (MQ=255)
                                                                    cAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGAtg                                                            <  1:2496620/134‑1 (MQ=255)
                                                                      gagagGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAACAGCCGAtgtg                                                          >  2:609911/1‑134 (MQ=255)
                                                                      gagagGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAAAGTTGCTTTACAAGGcactgtt                                                          >  2:2861902/1‑128 (MQ=255)
                                                                       agagGGATGGGATAAAATGAACTTTGTAACGTTGACTTCTGATGAGTTGAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGc                                                         <  1:1004123/134‑1 (MQ=255)
                                                                           ggatgggatAAAATGAACTTTGTAACGTTTACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCt                                                     <  1:358562/134‑1 (MQ=255)
                                                                           ggatgggatAAAATGAACTTTGTAACGTTGACTTCGGATTAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCt                                                     <  1:2356300/134‑1 (MQ=255)
                                                                            gatgagatgaAATGAACTTTGTAATGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGAGATGTGCAtttt                                                    <  2:258317/134‑1 (MQ=255)
                                                                                ggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTCCATCTTATAg                                                >  2:1704980/1‑134 (MQ=255)
                                                                                 gatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCAGTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAgg                                               <  1:2137818/134‑1 (MQ=255)
                                                                                 gatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAAGGCGTTTACTACAAAGCATTTTTCAACATGA‑ATACGATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAgg                                               <  2:1752593/134‑1 (MQ=255)
                                                                                  atAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATCGAGTTGATTTAAAAGGCGATGTGCATCTTTTCggg                                              >  2:2665659/1‑134 (MQ=255)
                                                                                   tAAAATGAACTTTGTAACGTTGACTTCTGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAgggg                                             <  1:1112431/134‑1 (MQ=255)
                                                                                   tAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACACAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAATGCGATGTGCATCTTGTAcggg                                             >  2:1919486/1‑134 (MQ=255)
                                                                                     aaaTGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGtt                                           <  2:2563029/134‑1 (MQ=255)
                                                                                     aaaTGAACTTTGTAACGGTGACTTCGGATGAGTTCAATGCGTTTAATACAAAGCATTTTTC‑ACATTACACAGAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGtt                                           <  2:438512/134‑1 (MQ=255)
                                                                                      aaTGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGATGATATAAAAAGCGATGTGCATCTTGTAGGGGTTa                                          >  1:1093631/1‑134 (MQ=255)
                                                                                       aTGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAAAGTTGATTTAAAAGGCAATGTACATGTTGTAGGGATTaa                                         >  2:2618104/1‑134 (MQ=255)
                                                                                         tatcTTTGTATCGTTTTCTTCGGATTAGTTCAATGCTTTTACTACAAAGCATCTTTA‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAg                                       <  1:923829/131‑1 (MQ=255)
                                                                                         gAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAg                                       <  2:1017446/134‑1 (MQ=255)
                                                                                           aCTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGAt                                     >  2:2681632/1‑134 (MQ=255)
                                                                                            cTTTGTAACGTTGACTTCTGATGAGTTCAATTTGTTTACGACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATg                                    <  1:2624028/134‑1 (MQ=255)
                                                                                              ttGTAACGTTGACTTCGTATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGAc                                  <  2:555751/134‑1 (MQ=255)
                                                                                               tGTAACGTTGACTTCGGATGAGTTCAATGTGTTTACTATAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACa                                 <  1:1787779/134‑1 (MQ=255)
                                                                                                gTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTCGAGGCGATAAATATGATaa                                <  2:631748/134‑1 (MQ=255)
                                                                                                gTAACGTTGACTTCGAATGAGTTTAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATTAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACaa                                <  2:387400/134‑1 (MQ=255)
                                                                                                 tAACGTTGACTTCGGATGATTTCAATGCGTTTACTACAAAGCATTTTTC‑ATATTACACACAATCAACTATTCATTACAATCATACAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAAt                               <  2:473591/134‑1 (MQ=255)
                                                                                                 tAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTTATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAAt                               <  1:2304047/134‑1 (MQ=255)
                                                                                                   aCGTTGACTTCGGATGAGTTCAATGCGTGTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAAAGTTGATTTAAAAGGCGATGTGCATATTGTAGGGGTTAAAGATGACAATgg                             >  1:590001/1‑134 (MQ=255)
                                                                                                    cGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGt                            <  2:1186670/134‑1 (MQ=255)
                                                                                                     gTTGACTTTGGATGAGGTAAATGCGTTTACTACAAAGCAATTTTA‑ACATTACAGACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGAAGTGCATTTTTTAGGGGTTAAAGATGACAATGGTc                           <  2:2806054/134‑1 (MQ=255)
                                                                                                      ttGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCa                          >  1:1901971/1‑134 (MQ=255)
                                                                                                      ttGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGAATCTTGTAGGAGTTAAAGATGACAATCGTCa                          >  2:2082487/1‑134 (MQ=255)
                                                                                                         aCTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑CCCTTCCCCACTCACAGCCATTCTTCACAATCATAGAGTTGATTTAAAAGGCGATTTGCATATTGTAGGAAATAAAGATGACAATGGTCAAgg                       >  1:675866/1‑133 (MQ=255)
                                                                                                          cTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTATAGGGGTTAAAGATGACAATGGTCAAgca                      >  2:746237/1‑132 (MQ=255)
                                                                                                          cTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATGCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTg                      <  1:2782537/134‑1 (MQ=255)
                                                                                                           ttCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGa                     >  2:881834/1‑134 (MQ=255)
                                                                                                              ggATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTg                  <  1:1515033/134‑1 (MQ=255)
                                                                                                               gATTAGTTCAATGCATTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGc                 <  1:2468384/134‑1 (MQ=255)
                                                                                                               gATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGTGATTCTGTACTGTTATCGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGCTTAAAGATGACAATAGTCAAGTGATTGc                 >  2:2173856/1‑134 (MQ=255)
                                                                                                               gATGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGc                 <  1:207896/134‑1 (MQ=255)
                                                                                                                aTGAGTTCAATGCGTTTACTACAAAGCATTTTTT‑ACATTACACACAATCAGCTATTCATTTCAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTACGGGTTAAAGATGACAATGGTCAAGTGATTGCa                <  2:2538048/134‑1 (MQ=255)
                                                                                                                 tGAGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGACGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAg               >  2:2316128/1‑134 (MQ=255)
                                                                                                                       ctaTGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGGTAAAGATGACAATGGTCAAGTGATTGCAGGATGCt         <  1:736155/132‑1 (MQ=255)
                                                                                                                         aTGCGTTTACTACAATTCATTTTTC‑ACATTACACACAATCAGTTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTa       <  1:2710013/134‑1 (MQ=255)
                                                                                                                         aTGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGTCATCGTTGACAGGCATAGAGTTGAATCAAAAGACGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTa       >  1:1970942/1‑134 (MQ=255)
                                                                                                                         aTGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTa       <  1:1587312/134‑1 (MQ=255)
                                                                                                                         aTGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTa       >  1:2660998/1‑134 (MQ=255)
                                                                                                                         aTGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTa       <  1:919617/134‑1 (MQ=255)
                                                                                                                         aTGCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGAGGTTAAAGATGACAATGGTCAAGTGATTGAAGGATGCTTa       >  2:915286/1‑134 (MQ=255)
                                                                                                                           gCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTAtt     <  1:1420317/134‑1 (MQ=255)
                                                                                                                           gCGTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCAAAGAGTTGATTTAAAAAACGATGTGCATATTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTAtt     >  1:69076/1‑134 (MQ=255)
                                                                                                                             gTTTACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGa   >  2:1495407/1‑134 (MQ=255)
                                                                                                                              tttACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGATTAAAGATGACAATGATCAAGTGATTGCAGGATGCTTATTCAc  >  2:1950933/1‑134 (MQ=255)
                                                                                                                              tttACTACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGATGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTAACGTGGTTGCAGGATGCTTATTGAc  >  1:1465281/1‑134 (MQ=255)
                                                                                                                                   |                                                                                                                                 
TTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTC‑ACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGAC  >  USA300TCH1516_ALE/2532167‑2532426

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A