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
A10 F112 I0 R1 51 112.5 5500062 95.1% 5230558 99.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 3,798,234 A→T 16.2% intergenic (+27/+5) waaL → / ← waaU O‑antigen ligase/lipopolysaccharide core biosynthesis

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,798,2340AT16.2% 349.9 / 54.9 135intergenic (+27/+5)waaL/waaUO‑antigen ligase/lipopolysaccharide core biosynthesis
Reads supporting (aligned to +/- strand):  ref base A (49/64);  new base T (12/10);  total (61/74)
Fisher's exact test for biased strand distribution p-value = 3.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.39e-01

Only 100 of 137 total aligned reads displayed.

TTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTGGGGATACTATTTGTA  >  NC_000913/3798137‑3798333
                                                                                                 |                                                                                                   
  ccAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGACGTGAGTTAAAAc                                                                                                 <  1:1806869/100‑1 (MQ=255)
  ccAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAAc                                                                                                 <  2:166564/100‑1 (MQ=255)
  ccAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAAc                                                                                                 >  1:2434036/1‑100 (MQ=255)
   cAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAAc                                                                                                 >  2:516230/1‑99 (MQ=255)
     aTTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCa                                                                                              <  2:2521369/100‑1 (MQ=255)
         tCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTTTAACTCActtc                                                                                          <  1:2328506/100‑1 (MQ=255)
           nttATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCActtctt                                                                                        >  1:1962844/2‑100 (MQ=255)
           aTTATATCCTCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCActtct                                                                                         <  2:579475/99‑1 (MQ=255)
           aTTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTTTAACTCActtctt                                                                                        >  2:59147/1‑100 (MQ=255)
           aTTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCActtctt                                                                                        <  2:2456487/100‑1 (MQ=255)
           aTTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTAActtctt                                                                                        >  2:2254287/1‑100 (MQ=255)
            ttATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTa                                                                                       <  1:2360064/100‑1 (MQ=255)
            ttATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTa                                                                                       <  1:1033827/100‑1 (MQ=255)
             tataTCCGCTATAGTCCTTTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTTTAACTCActtct                                                                                         <  2:1907669/97‑1 (MQ=39)
              atatCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTTTAACTCACTTCTTaaa                                                                                     <  2:2232780/100‑3 (MQ=255)
              atatCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATc                                                                                     <  1:2298060/100‑1 (MQ=255)
               tatCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTTTAACTCACTTCTTaaac                                                                                    <  1:59147/100‑4 (MQ=38)
               tatCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCt                                                                                    >  1:558308/1‑100 (MQ=255)
               tagctgCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATc                                                                                     <  2:2652822/94‑1 (MQ=255)
                atCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTGATTAAGAATAAACAAGTTTATGAAGTGAGTTAAAACTCACTTCTTATCta                                                                                   >  2:683094/1‑100 (MQ=255)
                atCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTTTAACTCACTTCTTaaact                                                                                   <  2:1996957/100‑5 (MQ=38)
                 tCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCtat                                                                                  <  1:2107902/100‑1 (MQ=255)
                    gCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACa                                                                               >  1:1031732/1‑100 (MQ=255)
                       ataGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACt                                                                            <  1:806212/100‑1 (MQ=255)
                          gTCCTCTTGCTCGTCATTAATAATCGTAAAAATACAATTAATTAAGAATAAACAACTTTAAGAAGCGAGCTAAAAATGACTTCTTATCtat                                                                                  >  2:2330482/1‑91 (MQ=255)
                            ccTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAAtc                                                                       >  2:2084626/1‑100 (MQ=255)
                              tctTACTCGTAATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTaa                                                                         <  2:1228854/96‑1 (MQ=255)
                               ctTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATctct                                                                    >  1:1079348/1‑100 (MQ=255)
                                ttACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCtt                                                                   <  1:2364924/100‑1 (MQ=255)
                                 tACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCttt                                                                  <  1:1331388/100‑1 (MQ=255)
                                   cTCGTCATTAATAAACGTAACAATAGAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACACACATCTAATATATACAAGTTAATctct                                                                    >  2:1228787/1‑96 (MQ=255)
                                     cGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTg                                                              <  1:705628/100‑1 (MQ=255)
                                     cGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTATTTACTg                                                              >  1:312860/1‑100 (MQ=255)
                                     cGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAATAAGTTAAAACTCACTTCTTATCTATACAACTTAATATCTTTACt                                                               >  2:2681542/1‑99 (MQ=255)
                                        cATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAAt                                                           <  2:1546046/100‑1 (MQ=255)
                                         aTTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAAtt                                                          <  1:1614388/100‑1 (MQ=255)
                                           taataaTCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAg                                                        >  2:2351369/1‑100 (MQ=255)
                                             ataatCGTACAAATACAATTAATTAAGAATAATTAAGTTTAAGAAGTGACTTATAACTTACTTCTTATCTATACAACTTAATTTCTGTACTGAATTAg                                                        <  2:1443086/98‑1 (MQ=255)
                                             ataatCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGtt                                                      <  2:1847954/100‑1 (MQ=255)
                                              taatCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTa                                                     >  1:2175047/1‑100 (MQ=255)
                                              taatCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTa                                                     >  1:1314166/1‑100 (MQ=255)
                                                 tCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAg                                                  <  2:558307/100‑1 (MQ=255)
                                                 tCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAg                                                  <  1:2196386/100‑1 (MQ=255)
                                                 tCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAg                                                  <  1:2215595/100‑1 (MQ=255)
                                                   gTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGACTTAGTTAAAGtt                                                >  1:379598/1‑100 (MQ=255)
                                                     aaCAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTc                                              <  1:865874/100‑1 (MQ=255)
                                                      acaatacaatTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCa                                             <  2:2128098/100‑1 (MQ=255)
                                                       caatacaatTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAg                                            >  1:1071931/1‑100 (MQ=255)
                                                       caatacaatTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAg                                            <  2:1136777/100‑1 (MQ=255)
                                                        aatacaatTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAg                                            <  2:1271686/99‑1 (MQ=255)
                                                        aatacaatTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGt                                           >  1:1434126/1‑100 (MQ=255)
                                                        aatacaatTAATTAAGAATAAACAACTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCa                                             <  2:1670103/98‑1 (MQ=255)
                                                            caatTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCg                                       <  1:2276434/100‑1 (MQ=255)
                                                            caatTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCg                                       >  1:1597839/1‑100 (MQ=255)
                                                            caatTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCg                                       >  2:2691450/1‑100 (MQ=255)
                                                             aattaattAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGa                                      <  2:1955348/100‑1 (MQ=255)
                                                             aattaattAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGa                                      <  1:582120/100‑1 (MQ=255)
                                                                 aattaaGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTCGTTAAAGTTTCAGTATCGATATc                                  >  1:2504497/1‑100 (MQ=255)
                                                                  attaaGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCt                                 <  1:1379605/100‑1 (MQ=255)
                                                                   ttaaGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCtt                                >  1:252333/1‑100 (MQ=255)
                                                                   ttaaGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCtt                                <  2:321533/100‑1 (MQ=255)
                                                                    taaGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCttt                               <  2:1071927/100‑1 (MQ=255)
                                                                    taaGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCttt                               >  1:1531534/1‑100 (MQ=255)
                                                                     aaGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCtttt                              >  2:233826/1‑100 (MQ=255)
                                                                     aaGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCtttt                              <  1:1009085/100‑1 (MQ=255)
                                                                      aGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTa                             >  1:1904061/1‑100 (MQ=255)
                                                                      aGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTa                             <  1:2705775/100‑1 (MQ=255)
                                                                       gAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTAc                            <  1:1710320/100‑1 (MQ=255)
                                                                          tAAACGAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAATTAAAGATTCAGTATCGATATCTTTTACCgc                         >  2:113046/1‑99 (MQ=255)
                                                                           aaaCAAGTTTAAGAAGTGAGTTAAAACACACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGta                        >  2:1577672/1‑100 (MQ=255)
                                                                            aaCAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGtat                       >  2:1398583/1‑100 (MQ=255)
                                                                            aaCAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGtat                       >  2:1377598/1‑100 (MQ=255)
                                                                             aCAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGtata                      <  2:942794/100‑1 (MQ=255)
                                                                              cAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTatat                     >  1:1772801/1‑100 (MQ=255)
                                                                              cAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTatat                     >  2:2436477/1‑100 (MQ=255)
                                                                                 gTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGtt                  >  2:1880822/1‑100 (MQ=255)
                                                                                 gTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGtt                  >  1:585681/1‑100 (MQ=255)
                                                                                   ttAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTgg                <  1:1271096/100‑1 (MQ=255)
                                                                                   ttAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTgg                <  1:853751/100‑1 (MQ=255)
                                                                                   ttAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTAACGTATATGTTgg                >  2:1291388/1‑100 (MQ=255)
                                                                                    tAAGAAGTGAGTTTTAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTggg               >  1:155250/1‑100 (MQ=255)
                                                                                    tAAGAAGTGAGTTTTAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTggg               >  2:2080065/1‑100 (MQ=255)
                                                                                    tAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTggg               <  1:746530/100‑1 (MQ=255)
                                                                                     aagaagTGAGTTTTAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTgggg              >  1:577517/1‑100 (MQ=255)
                                                                                     aagaagTGAGTTAAACCTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTgggg              <  1:2706263/100‑1 (MQ=255)
                                                                                     aagaagTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTgggg              <  2:1454365/100‑1 (MQ=255)
                                                                                      agaagTGAGTTTTAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTGGTGa             >  2:375124/1‑100 (MQ=255)
                                                                                      agaagTGAGTTTTAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTGGGGa             >  2:1357643/1‑100 (MQ=255)
                                                                                      agaagTGAGTTTTAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACAGTATATGTTgtgca             >  2:1663525/1‑96 (MQ=39)
                                                                                      agaagTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTGGGGa             <  1:616314/100‑1 (MQ=255)
                                                                                       gaagTGAGTTTTAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTGGGGAt            >  2:288034/1‑100 (MQ=255)
                                                                                          gTGAGTTTTAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTGGGGATACt         >  2:866024/1‑100 (MQ=255)
                                                                                          gTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTGGGGATACt         <  1:2028198/100‑1 (MQ=255)
                                                                                              gTTAAAACTCACTTCTTATTTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTGTCAGTATCGATATCTTTTACCGTATATGTTGGGGATACTAtt      <  2:698231/99‑1 (MQ=255)
                                                                                              gTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAATTTTCAGTATCGATATTTTTTACCGTATATGTTGGGGATACTAtt      >  2:1609367/1‑99 (MQ=255)
                                                                                              gTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTGGGGATACTAttt     >  2:1247431/1‑100 (MQ=255)
                                                                                              gTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTGGGGATACTAttt     >  2:696017/1‑100 (MQ=255)
                                                                                               ttAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTGGGGATACTATTTg    <  1:1908835/100‑1 (MQ=255)
                                                                                               ttAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTGGGGATACTATTTg    <  2:2276745/100‑1 (MQ=255)
                                                                                                 aaaaCTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTGGGGATACTATTTGta  <  1:371008/100‑1 (MQ=255)
                                                                                                 |                                                                                                   
TTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTAAGAAGTGAGTTAAAACTCACTTCTTATCTATACAACTTAATCTCTTTACTGAATTAGTTAAAGTTTCAGTATCGATATCTTTTACCGTATATGTTGGGGATACTATTTGTA  >  NC_000913/3798137‑3798333

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