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
A7 F422 I52 R1 239 220.4 11079197 93.2% 10325811 100.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 394,041 T→G pseudogene (1072/1449 nt) yaiT → pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913394,0410TG98.5% 678.3 / ‑0.8 195pseudogene (1072/1449 nt)yaiTpseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
Reads supporting (aligned to +/- strand):  ref base T (2/1);  new base G (96/96);  total (98/97)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.49e-01

Only 100 of 195 total aligned reads displayed.

TACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTTACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCAGTCTTACGACAGCATGCGTTAT  >  NC_000913/393944‑394136
                                                                                                 |                                                                                               
tACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGAc                                                                                               <  1:2366237/100‑1 (MQ=255)
 aCTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACg                                                                                              <  2:1640091/100‑1 (MQ=255)
  cTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACgg                                                                                             >  1:192981/1‑100 (MQ=255)
  cTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACgg                                                                                             >  2:2710063/1‑100 (MQ=255)
   ttACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGTCTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGc                                                                                            <  2:2406806/100‑1 (MQ=255)
    tACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCa                                                                                           >  1:413426/1‑100 (MQ=255)
    tACGTTGACGGTAGCACCAACTCCGACGCTTACGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACAGGGTGATGCTGGTTACGTGACTCCTGACGGCa                                                                                           >  2:326533/1‑100 (MQ=255)
    tACGCTGCCGGTAGCACCAACTCCGACGCGTGGGGCTTCGGTTTGAAAGCCGGGTATGACTTCAAACTGGGTGATGCTGGATACGTGACTCCTGACGGCa                                                                                           >  2:4526720/1‑100 (MQ=255)
       gTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCg                                                                                        <  1:2909338/100‑1 (MQ=255)
         tGACGGTAGCAGCAACTCCGACGCTTGGGGCTTCGGTTTGTAAGCCGGTTACGACTTCAAACTGGGTGATGTTGGTTACGTGACTCTTGACGGCAGCGtt                                                                                      <  1:4909403/100‑1 (MQ=255)
         tGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGtt                                                                                      <  2:2687695/100‑1 (MQ=255)
         tGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGtt                                                                                      <  2:1822499/100‑1 (MQ=255)
            cGGTAGTACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCt                                                                                   >  1:842422/1‑100 (MQ=255)
            cGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCt                                                                                   <  1:1042451/100‑1 (MQ=255)
             ggTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTg                                                                                  >  2:651752/1‑100 (MQ=255)
             ggTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTg                                                                                  >  2:108575/1‑100 (MQ=255)
                   aCCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGt                                                                            <  2:4669038/100‑1 (MQ=255)
                   aCCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGt                                                                            <  1:941984/100‑1 (MQ=255)
                     cAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTc                                                                          >  1:5001822/1‑100 (MQ=255)
                      aaCTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTcc                                                                         <  2:5216278/100‑1 (MQ=255)
                        cTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAg                                                                       <  2:4998796/100‑1 (MQ=255)
                        cTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAg                                                                       >  2:4380713/1‑100 (MQ=255)
                             aCGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTgg                                                                  <  2:4288045/100‑1 (MQ=255)
                              cGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGt                                                                 <  2:4218184/100‑1 (MQ=255)
                              cGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGt                                                                 >  1:54195/1‑100 (MQ=255)
                              cGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGt                                                                 >  1:55726/1‑100 (MQ=255)
                               gCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGtg                                                                <  2:514878/100‑1 (MQ=255)
                               gCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGtg                                                                >  2:3444612/1‑100 (MQ=255)
                               gCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACAGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGtg                                                                <  2:2430365/100‑1 (MQ=255)
                                cTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTTACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGtga                                                               >  1:4592060/1‑100 (MQ=255)
                                cTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGtga                                                               >  2:2254794/1‑100 (MQ=255)
                                cTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGtga                                                               <  2:3906885/100‑1 (MQ=255)
                                 ttGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGtgat                                                              >  2:781156/1‑100 (MQ=255)
                                 ttGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGtgat                                                              >  2:4031571/1‑100 (MQ=255)
                                 ttGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGtgat                                                              <  2:4355698/100‑1 (MQ=255)
                                 ttGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGtgat                                                              <  2:5442693/100‑1 (MQ=255)
                                   ggggCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGtgatga                                                            >  1:3531865/1‑100 (MQ=255)
                                   ggggCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGtgatga                                                            <  2:4985966/100‑1 (MQ=255)
                                   ggggCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTAAGTGACTCATGACGGCAGCGTTTCTGGTCTGTTCTAGTCTGGtgatga                                                            >  2:2754728/1‑100 (MQ=255)
                                    gggCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGAc                                                           >  2:213181/1‑100 (MQ=255)
                                    gggCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGAc                                                           <  2:2560466/100‑1 (MQ=255)
                                    gggCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGAc                                                           >  2:1314444/1‑100 (MQ=255)
                                     ggCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACt                                                          >  1:5041291/1‑100 (MQ=255)
                                     ggCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACt                                                          >  2:149421/1‑100 (MQ=255)
                                      gCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTCCTGGTCTGTTCCAGTCTGGTGATGACTa                                                         >  2:4107172/1‑100 (MQ=255)
                                        ttCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTAcc                                                       <  2:623203/100‑1 (MQ=255)
                                        ttCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTAcc                                                       <  2:4774778/100‑1 (MQ=255)
                                          cGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAg                                                     >  2:169872/1‑100 (MQ=255)
                                          cGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAg                                                     >  1:4159425/1‑100 (MQ=255)
                                           ggTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGc                                                    >  1:180555/1‑100 (MQ=255)
                                           ggTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCAGGTTACGTGCCTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGc                                                    >  1:183965/1‑100 (MQ=255)
                                            gTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCt                                                   >  2:3832899/1‑100 (MQ=255)
                                            gTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTATCTGGTCTGTTCCAGTCTGGTGATGCCTACCAGCt                                                   >  2:4621193/1‑100 (MQ=255)
                                             tttGAAAGCCGGTTACGACTTCTAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTg                                                  <  1:5159213/100‑1 (MQ=255)
                                              ttGAAAGCCGGTTACGACGTCAACCTGGGTGATGCTGGTTACGTGGCTGCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGa                                                 <  2:4564723/100‑1 (MQ=255)
                                               tGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAg                                                <  1:1467445/100‑1 (MQ=255)
                                                gAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGc                                               >  2:2033447/1‑100 (MQ=255)
                                                   aGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAAc                                            <  2:4823314/100‑1 (MQ=255)
                                                   aGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAAc                                            <  2:4652262/100‑1 (MQ=255)
                                                     ccGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGa                                          >  1:2606846/1‑100 (MQ=255)
                                                      cGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGAc                                         <  1:3666993/100‑1 (MQ=255)
                                                      cGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGAc                                         <  2:3735532/100‑1 (MQ=255)
                                                       ggTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACa                                        <  1:2203325/100‑1 (MQ=255)
                                                        gTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACAt                                       <  1:2003720/100‑1 (MQ=255)
                                                         ttACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATg                                      <  2:3645542/100‑1 (MQ=255)
                                                         ttACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATg                                      <  1:5520484/100‑1 (MQ=255)
                                                            cGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGaaa                                   >  1:3499734/1‑100 (MQ=255)
                                                             gACTTCAAACTGGGTTATGCTGGTTACTTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAg                                  <  2:1887238/100‑1 (MQ=255)
                                                             gACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTTACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAg                                  <  1:4261158/100‑1 (MQ=255)
                                                               cTTCAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGtt                                >  1:826041/1‑100 (MQ=255)
                                                                  cAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACCTGAAAGTTgtc                             <  2:5091976/100‑3 (MQ=255)
                                                                  cAAACTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGAc                             <  1:4496861/100‑1 (MQ=255)
                                                                   aaaCTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACg                            <  1:171542/100‑1 (MQ=255)
                                                                    aaCTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACgg                           <  1:4733157/100‑1 (MQ=255)
                                                                      cTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTc                         <  1:3886897/100‑1 (MQ=255)
                                                                      cTGGGTGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTc                         >  1:3951013/1‑100 (MQ=255)
                                                                       tGGGTGATGCTGGTCACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCa                        >  1:133140/1‑100 (MQ=255)
                                                                          gttaTGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCAGTc                     <  2:4719509/97‑1 (MQ=255)
                                                                          gTGATGCTGGTTACCTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCAGTc                     <  1:5238676/100‑1 (MQ=255)
                                                                           tGATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCAGTCt                    >  1:3197009/1‑100 (MQ=255)
                                                                            gATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCAGTCtt                   >  1:1220990/1‑100 (MQ=255)
                                                                            gATGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCAGTCtt                   >  2:5100702/1‑100 (MQ=255)
                                                                             atgatgGTTCAGTGACTCCTGAAGGAAGAGTTTCTGGTCTGTTACAGTCTGGTGATGACTACCAGCTGAGCAACGACATGCAAGTTGACGGTCAGTCTTa                  <  2:250018/100‑1 (MQ=255)
                                                                             aTGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCAGTCTTa                  <  1:1494599/100‑1 (MQ=255)
                                                                             aTGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCAGTCTTa                  <  2:1965809/100‑1 (MQ=255)
                                                                             aTGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCAGTCTTa                  <  1:2524865/100‑1 (MQ=255)
                                                                             aTGCTGGTTACGTAACTCCTGACGGCCGCGTTTCGGGTCTGTTCCGCTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCAGTCTTa                  <  2:3529851/100‑1 (MQ=255)
                                                                              tGCTGGTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCAGTCTTAc                 <  1:2781224/100‑1 (MQ=255)
                                                                               gCTGGTTACGTGACTCCTGACGGCAGCATCTCTGGTCTGTAACACTCTGGTGATGACTACTAGCTGAGGAACGACATCAATGTTAACGGCAAGACTTACg                >  2:506417/1‑100 (MQ=255)
                                                                                 nggTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCAGTCTTACGAc              >  1:1749397/2‑100 (MQ=255)
                                                                                  ggTTACGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCAGTCTTACGACa             >  1:1682979/1‑100 (MQ=255)
                                                                                     tACGTGACTCCTGACGGCAGAGTTTCTGGTATGTTCCAGTCTGGTGATGACTACAAGCAGAGCAAAGAATTGAAAGTTGACGGTCAGTCTTAAGACAGCa          >  2:955713/1‑100 (MQ=255)
                                                                                       cGTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCAGTCTTACGACAGCATg        >  2:3590637/1‑100 (MQ=255)
                                                                                        gTGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTAGCAGCTGAGCAACGTCATGAAAGTTGACGGTCAGTCTTACGACAGCATGc       >  2:5421793/1‑100 (MQ=255)
                                                                                         tGACTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCAGTCTTACGACAGCATGCg      <  1:3074656/100‑1 (MQ=255)
                                                                                           aCTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCAGTCTTACGACAGCATGCGtt    <  1:4712872/100‑1 (MQ=255)
                                                                                            cTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGGGCAACGACATGAAAGTTGACGGTCAGTCTTACGACAGCATGCGTTa   >  2:3020070/1‑100 (MQ=255)
                                                                                            cTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCAGTCTTACGACAGCATGCGTTa   >  1:43745/1‑100 (MQ=255)
                                                                                            cTCCTGACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCAGTCTTACGACAGCATGCGTTa   <  1:635868/100‑1 (MQ=255)
                                                                                            cTCCTGACGGCAGCGTTTCTCGTCTGATCCAGTCTGGTGGTGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCAGTCTTACGACAGCATGCGTTa   <  1:5214827/100‑1 (MQ=255)
                                                                                                 |                                                                                               
TACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCAAACTGGGTGATGCTGGTTACGTGACTCCTTACGGCAGCGTTTCTGGTCTGTTCCAGTCTGGTGATGACTACCAGCTGAGCAACGACATGAAAGTTGACGGTCAGTCTTACGACAGCATGCGTTAT  >  NC_000913/393944‑394136

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A