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
A0 F0 I0 R1 26 340.5 11737388 98.1% 11514377 90.8

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% 1311.9 / ‑6.5 330T15T (ACA→ACT) femA_3Aminoacyltransferase FemA
Reads supporting (aligned to +/- strand):  ref base A (1/0);  major base T (139/189);  minor base G (1/0);  total (141/189)
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 343 total aligned reads displayed.

AAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGT  >  USA300TCH1516_ALE/2532211‑2532384
                                                                                       |                                                                                      
aaaTTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTactaca                                                                                     >  2:4323833/1‑91 (MQ=255)
aaaTTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTactaca                                                                                     >  2:52005/1‑91 (MQ=255)
 aaTTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTActacaa                                                                                    <  2:2050149/91‑1 (MQ=255)
 aaTTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTActacaa                                                                                    <  1:724492/91‑1 (MQ=255)
 aaTTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTActacaa                                                                                    >  2:4549345/1‑91 (MQ=255)
  aTTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACaaa                                                                                   <  2:2696498/91‑1 (MQ=255)
  aTTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACaaa                                                                                   <  2:368056/91‑1 (MQ=255)
   ttCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAg                                                                                  <  1:5787077/91‑1 (MQ=255)
    tCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGc                                                                                 >  2:4814437/1‑91 (MQ=255)
       aaaaTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAtt                                                                              >  1:1571713/1‑91 (MQ=255)
       aaaaTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAtt                                                                              >  1:1741226/1‑91 (MQ=255)
        aaaTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAttt                                                                             <  1:3846726/91‑1 (MQ=255)
        aaaTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAttt                                                                             <  1:5485984/91‑1 (MQ=255)
        aaaTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAttt                                                                             >  1:2413111/1‑91 (MQ=255)
         aaTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAGCTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAtttt                                                                            <  1:4851079/91‑1 (MQ=255)
         aaTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAtttt                                                                            <  1:628018/91‑1 (MQ=255)
         aaTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAtttt                                                                            >  1:5126737/1‑91 (MQ=255)
          aTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAttttt                                                                           <  2:1677954/91‑1 (MQ=255)
            tataGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCGATGCGTTTACTACAAAGCATTTTTca                                                                         >  2:5309616/1‑91 (MQ=255)
             ataGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTcac                                                                        >  1:3367686/1‑91 (MQ=255)
               aGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACAt                                                                      <  1:5598135/91‑1 (MQ=255)
               aGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACAt                                                                      >  1:2655279/1‑91 (MQ=255)
               aGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACAt                                                                      <  1:2119011/91‑1 (MQ=255)
                gTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACAtt                                                                     >  2:726902/1‑91 (MQ=255)
                gTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACAtt                                                                     >  2:5581994/1‑91 (MQ=255)
                gTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACAtt                                                                     >  2:5509001/1‑91 (MQ=255)
                 ttCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTa                                                                    <  2:218208/91‑1 (MQ=255)
                  tCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTac                                                                   >  1:1185733/1‑91 (MQ=255)
                  tCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTac                                                                   <  2:5000222/91‑1 (MQ=255)
                  tCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTac                                                                   <  1:1658858/91‑1 (MQ=255)
                   cAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTaca                                                                  <  2:3202543/91‑1 (MQ=255)
                    aaTTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTacac                                                                 <  2:3585869/91‑1 (MQ=255)
                      ttCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTacacac                                                               <  2:5426827/91‑1 (MQ=255)
                        cAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACaa                                                             <  2:1745103/91‑1 (MQ=255)
                           agagGGATGGGATAATATGAACTTTGTAACGTTGACTTCGGATGACTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACAGAATCa                                                          <  2:5741444/91‑1 (MQ=255)
                           agagGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCa                                                          >  1:3218002/1‑91 (MQ=255)
                            gagGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAg                                                         <  2:3336266/91‑1 (MQ=255)
                             agGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGc                                                        <  1:3494464/91‑1 (MQ=255)
                             agGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGc                                                        <  1:1444009/91‑1 (MQ=255)
                                 atgggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTAtt                                                    <  1:5410331/91‑1 (MQ=255)
                                  tgggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCTGCTATTc                                                   >  2:3954220/1‑91 (MQ=255)
                                  tgggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTc                                                   <  2:4058704/91‑1 (MQ=255)
                                  tgggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTc                                                   <  1:804043/91‑1 (MQ=255)
                                  tgggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTc                                                   <  1:5671334/91‑1 (MQ=255)
                                   gggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCa                                                  >  1:3707744/1‑91 (MQ=255)
                                    ggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCGTTTTTCACATTACACACAATCAGCTATACAt                                                 >  1:5449124/1‑91 (MQ=255)
                                    ggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCAt                                                 <  1:4471311/91‑1 (MQ=255)
                                      atAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTa                                               >  2:4604168/1‑91 (MQ=255)
                                        aaaaTGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTACTCATTACa                                             >  1:2271631/1‑91 (MQ=255)
                                         aaaTGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCTTTTTTCTCTCTATCAGCTATTCATTACaa                                            >  2:2907990/1‑91 (MQ=255)
                                          aaTGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAt                                           >  1:4209422/1‑91 (MQ=255)
                                          aaTGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAt                                           >  1:1980444/1‑91 (MQ=255)
                                          aaTGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAt                                           >  2:2637651/1‑91 (MQ=255)
                                            tGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCa                                         <  2:856158/91‑1 (MQ=255)
                                            tGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGGTTACTACAAAGCATTTTGCACATTACACACAATGAGCTAGTCATTACAATCa                                         >  1:260411/1‑91 (MQ=255)
                                             gAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCAt                                        <  2:3071990/91‑1 (MQ=255)
                                             gAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCAt                                        <  1:2694296/91‑1 (MQ=255)
                                             gAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCAt                                        <  1:2523319/91‑1 (MQ=255)
                                              aaCTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCa                                         <  1:5285240/89‑1 (MQ=255)
                                              aaCTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATa                                       <  1:413498/91‑1 (MQ=255)
                                              aaCTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATa                                       >  2:3057212/1‑91 (MQ=255)
                                               aCTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCa                                         >  1:1113615/1‑88 (MQ=255)
                                               aCTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCa                                         <  2:1113615/88‑1 (MQ=255)
                                                cTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATaga                                     >  1:1788327/1‑91 (MQ=255)
                                                 tttGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATagag                                    <  1:1042509/91‑1 (MQ=255)
                                                  ttGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGt                                   >  2:1556579/1‑91 (MQ=255)
                                                  ttGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGt                                   <  2:249733/91‑1 (MQ=255)
                                                   tGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATagagat                                  >  1:1869611/1‑89 (MQ=255)
                                                   tGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGtt                                  >  2:36323/1‑91 (MQ=255)
                                                   tGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGtt                                  <  2:4465606/91‑1 (MQ=255)
                                                   tGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGtt                                  >  1:2860482/1‑91 (MQ=255)
                                                    gTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTg                                 <  1:3228934/91‑1 (MQ=255)
                                                      aaCGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGAt                               >  1:3318375/1‑91 (MQ=255)
                                                       aCGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGAtt                              >  1:5348062/1‑91 (MQ=255)
                                                        cGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGAttt                             <  1:5584875/91‑1 (MQ=255)
                                                        cGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGAttt                             >  1:4992039/1‑91 (MQ=255)
                                                          ttGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTaa                           <  1:3081863/91‑1 (MQ=255)
                                                          ttGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTaa                           >  2:437873/1‑91 (MQ=255)
                                                          ttGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTaa                           >  1:3801256/1‑91 (MQ=255)
                                                                tCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCg                     >  1:4549264/1‑91 (MQ=255)
                                                                tCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCg                     >  2:642233/1‑91 (MQ=255)
                                                                 ctgATTAGTTCAATGCGTTTAGTCTGTACTATCTTTCATATTACATACAATCAGCTATTCGTTACAAGCATATAGTTGATTTAAAAGGcca                    <  2:5657007/89‑3 (MQ=255)
                                                                 cGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGa                    <  2:4186853/91‑1 (MQ=255)
                                                                  ggATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGAt                   >  1:2368880/1‑91 (MQ=255)
                                                                   gATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGAtg                  <  2:1507401/91‑1 (MQ=255)
                                                                    aTGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGAtgt                 <  1:2763171/91‑1 (MQ=255)
                                                                    aTGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGAtgt                 <  2:951160/91‑1 (MQ=255)
                                                                      gAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGc               <  1:2012172/91‑1 (MQ=255)
                                                                      gAGTTCAATGCGATTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGc               <  2:1986220/91‑1 (MQ=255)
                                                                        gTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCAt             <  2:4706611/91‑1 (MQ=255)
                                                                        gTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCAt             <  1:467418/91‑1 (MQ=255)
                                                                        gTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCAt             >  2:1373343/1‑91 (MQ=255)
                                                                        gTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCAt             >  2:1814013/1‑91 (MQ=255)
                                                                        gTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCAt             <  2:1900123/91‑1 (MQ=255)
                                                                         ttCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATc            <  2:1030426/91‑1 (MQ=255)
                                                                             aTGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGt        <  1:3972700/91‑1 (MQ=255)
                                                                              tGCGTTTACTACAAAGCATTTTTCACATTACACACAATAAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTa       <  1:1262939/91‑1 (MQ=255)
                                                                               gCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAg      <  1:296935/91‑1 (MQ=255)
                                                                                 gTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAggg    <  1:4814437/91‑1 (MQ=255)
                                                                                  tttACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAgggg   >  2:4144293/1‑91 (MQ=255)
                                                                                       |                                                                                      
AAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGT  >  USA300TCH1516_ALE/2532211‑2532384

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A