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
A15 F141 I1 R1 21 114.5 4481172 94.2% 4221264 126.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_pae_tpiA 1,544,022 1 bp→AA coding (39/1389 nt) narU ← nitrate/nitrite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA1,544,0211.A83.3% 387.8 / 72.2 126coding (40/1389 nt)narUnitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base . (11/10);  new base A (55/50);  total (66/60)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01
*NC_000913_3_pae_tpiA1,544,0220CA96.8% 442.9 / 0.7 126L13F (TTG→TTT) narUnitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base C (2/2);  new base A (64/58);  total (66/60)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

Only 100 of 132 total aligned reads displayed.

TGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑C‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAA  >  NC_000913_3_pae_tpiA/1543880‑1544170
                                                                                                                                                |||                                                                                                                                                    
tGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGGTTCCAGTCGC‑G‑A‑a‑aaaaga                                                                                                                                               <  3:555264/150‑4 (MQ=255)
           gTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTTTTTTCCCATAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTAtt                                                                                                                                     >  2:269202/1‑150 (MQ=255)
              aCTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTAttttt                                                                                                                                  <  2:68895/150‑1 (MQ=255)
                     tAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCAttt                                                                                                                           >  1:540559/1‑150 (MQ=255)
                         tAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCa                                                                                                                       <  1:681649/150‑1 (MQ=255)
                          aGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAg                                                                                                                      >  3:370693/1‑150 (MQ=255)
                            cctCCAGACACAGAAGGCAAGAAGTAGACAACTGAGTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTAGC‑G‑A‑ATAAAGATAACGACTATTTTTCTCATTTTGCAGTg                                                                                                                    <  2:697331/148‑1 (MQ=255)
                            cATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑C‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGc                                                                                                                   <  3:551790/150‑1 (MQ=255)
                              tCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGcc                                                                                                                  >  3:232366/1‑150 (MQ=255)
                                cAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCat                                                                                                                >  1:1208881/1‑150 (MQ=255)
                                cAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑C‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCata                                                                                                               <  3:832375/150‑1 (MQ=255)
                                     acaGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGt                                                                                                           >  3:272546/1‑150 (MQ=255)
                                      caGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGtt                                                                                                          <  1:321765/150‑1 (MQ=255)
                                       aGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTTGATTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑AAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTc                                                                                                         <  1:25028/150‑1 (MQ=255)
                                       aGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTc                                                                                                         >  3:130987/1‑150 (MQ=255)
                                         aaGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCt                                                                                                       >  1:908872/1‑150 (MQ=255)
                                         aaGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCt                                                                                                       >  1:1327698/1‑150 (MQ=255)
                                            gCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTcac                                                                                                    >  2:1209200/1‑150 (MQ=255)
                                             cAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTcaca                                                                                                   <  4:370693/150‑1 (MQ=255)
                                              aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACAt                                                                                                  >  1:454657/1‑150 (MQ=255)
                                              aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACAt                                                                                                  >  1:651180/1‑150 (MQ=255)
                                                gaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGc                                                                                                >  3:451564/1‑150 (MQ=255)
                                                  agTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGcac                                                                                              <  2:1208881/150‑1 (MQ=255)
                                                   gTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGca                                                                                               <  2:1350130/148‑1 (MQ=255)
                                                   gTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGca                                                                                               >  1:1350130/1‑148 (MQ=255)
                                                      gACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACAt                                                                                          <  4:451564/150‑1 (MQ=255)
                                                      gACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTAAAAAAAA‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACAt                                                                                          <  2:67553/150‑1 (MQ=255)
                                                        cAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTTTCTA‑A‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTg                                                                                        <  3:446440/150‑1 (MQ=255)
                                                        cAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTg                                                                                        <  2:454657/150‑1 (MQ=255)
                                                         aaCTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTgg                                                                                       <  1:189287/150‑1 (MQ=255)
                                                          actgactgATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACCCATTGGt                                                                                      <  4:248013/150‑1 (MQ=255)
                                                            tgactgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑AAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTaa                                                                                    >  2:1312579/1‑150 (MQ=255)
                                                               ctgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGa                                                                                 <  1:877758/150‑1 (MQ=255)
                                                                  atatCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGc                                                                                                <  1:1269162/132‑1 (MQ=255)
                                                                  atatCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑AAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGc                                                                                                >  2:1269162/1‑132 (MQ=255)
                                                                    atCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaa                                                                            <  1:1209200/150‑1 (MQ=255)
                                                                    atCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaa                                                                            >  2:906755/1‑150 (MQ=255)
                                                                    atCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaa                                                                            >  4:28388/1‑150 (MQ=255)
                                                                      ccAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAg                                                                          >  2:910271/1‑150 (MQ=255)
                                                                      ccAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑A‑a‑aaaa                                                                                                                                                 <  3:657741/78‑2 (MQ=255)
                                                                        agagATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTgg                                                                                       >  1:441159/1‑135 (MQ=255)
                                                                        agagATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTgg                                                                                       <  2:441159/135‑1 (MQ=255)
                                                                        agagATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGAc                                                                        >  1:231857/1‑150 (MQ=255)
                                                                              ttcttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGa                                                                                                                                          >  2:162442/1‑78 (MQ=255)
                                                                              ttcttcGAGCAATATGTTTTCCTTTATTTTACCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑AAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAaca                                                                  >  3:627512/1‑150 (MQ=255)
                                                                               tcttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAacac                                                                 <  2:908872/150‑1 (MQ=255)
                                                                               tcttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCATCACATGCACACATTGGTAATGAAAAAAAGACAAAacac                                                                 >  3:725414/1‑150 (MQ=255)
                                                                                cttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACg                                                                >  1:614810/1‑150 (MQ=255)
                                                                                 ttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGGCTATTTTTCTCATTTTGCAGTGCCata                                                                                                               >  4:302043/1‑102 (MQ=255)
                                                                                 ttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGGCTATTTTTCTCATTTTGCAGTGCCata                                                                                                               <  3:302043/102‑1 (MQ=255)
                                                                                 ttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGa                                                               <  2:790575/150‑1 (MQ=255)
                                                                                   cGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGTCGGATTTTCTGGTTTCCAGTCGC‑G‑A‑a‑aaa                                                                                                                                                  >  3:441947/1‑64 (MQ=255)
                                                                                   cGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGTCGGATTTTCTGGTTTCCAGTCGC‑G‑A‑a‑aaa                                                                                                                                                  <  4:441947/64‑1 (MQ=255)
                                                                                      gCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTaa                                                          <  4:455741/150‑1 (MQ=255)
                                                                                       cAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATg                                                                                  >  3:617425/1‑125 (MQ=255)
                                                                                       cAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATg                                                                                  <  4:617425/125‑1 (MQ=255)
                                                                                       cAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAg                                                         <  1:84215/150‑1 (MQ=255)
                                                                                          tatGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTc                                                                                                         <  2:1124652/99‑1 (MQ=255)
                                                                                          tatGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTc                                                                                                         >  1:1124652/1‑99 (MQ=255)
                                                                                              ttttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAAt                                                  >  4:566979/1‑150 (MQ=255)
                                                                                              ttttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑AAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAAt                                                  >  2:783163/1‑150 (MQ=255)
                                                                                               tttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATa                                                 >  1:627760/1‑150 (MQ=255)
                                                                                               cttCCTTTATTTACCCAGAAGGCCGGATTTTCTGGTTTCCAGTAGC‑GAA‑A‑AAAGATAACGATTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCATAAAAAAAAAAAAAAAAAAAGACAAAACACGAGGTAAGGCGCAATa                                                 <  2:1191133/149‑1 (MQ=255)
                                                                                                   cTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAACATCAGAAGAGGCCCGAGGTAAGGCGCAATAGCCa                                             >  1:748455/1‑150 (MQ=255)
                                                                                                   cTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa                                             <  1:1189958/150‑1 (MQ=255)
                                                                                                    tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCa                                                                                                                       >  1:1007154/1‑75 (MQ=255)
                                                                                                    tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCa                                                                                                                       <  2:1007154/75‑1 (MQ=255)
                                                                                                    tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGgc                                                       <  3:778755/139‑1 (MQ=255)
                                                                                                    tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGgc                                                       >  4:778755/1‑139 (MQ=255)
                                                                                                     ttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAgg                                                        >  2:278523/1‑137 (MQ=255)
                                                                                                       aTTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGtta                                         >  1:1387108/1‑150 (MQ=255)
                                                                                                         tttCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaaa                                                                           <  3:326934/114‑1 (MQ=255)
                                                                                                         tttCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaaa                                                                           >  4:326934/1‑114 (MQ=255)
                                                                                                         tttCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGttatt                                       <  2:670748/150‑1 (MQ=255)
                                                                                                         tttCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGttatt                                       <  3:566979/150‑1 (MQ=255)
                                                                                                             ccAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGaa                                   <  4:725414/150‑1 (MQ=255)
                                                                                                             ccAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGaa                                   >  3:782192/1‑150 (MQ=255)
                                                                                                                gAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTa                                <  3:28388/150‑1 (MQ=255)
                                                                                                                    gCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGa                            >  3:610173/1‑150 (MQ=255)
                                                                                                                     ccGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaaa                                                                           <  1:558510/102‑1 (MQ=255)
                                                                                                                     ccGGATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaaa                                                                           >  2:558510/1‑102 (MQ=255)
                                                                                                                       ggATTTTCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGa                         >  3:606519/1‑150 (MQ=255)
                                                                                                                          ttttCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAAtt                      <  2:775765/150‑1 (MQ=255)
                                                                                                                           tttCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTg                     <  2:540559/150‑1 (MQ=255)
                                                                                                                            ttCTGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATCTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTgg                    <  2:515531/150‑1 (MQ=255)
                                                                                                                               tGGTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTg                 <  2:614810/150‑1 (MQ=255)
                                                                                                                                ggTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaaa                                                                           >  4:282357/1‑91 (MQ=255)
                                                                                                                                ggTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaaa                                                                           <  3:282357/91‑1 (MQ=255)
                                                                                                                                 gTTTCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGaa               >  2:1085425/1‑150 (MQ=255)
                                                                                                                                  tttCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTcac                                                                                                    >  2:1119636/1‑64 (MQ=255)
                                                                                                                                  tttCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTcac                                                                                                    <  1:1119636/64‑1 (MQ=255)
                                                                                                                                   ttCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGt             >  1:663399/1‑150 (MQ=255)
                                                                                                                                    tCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTg                     >  3:669894/1‑141 (MQ=255)
                                                                                                                                    tCCAGTCGC‑GAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTg                     <  4:669894/141‑1 (MQ=255)
                                                                                                                                       aGTCGC‑G‑AAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTg         >  2:347395/1‑150 (MQ=255)
                                                                                                                                             gcgaaa‑aaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTg     <  1:714162/145‑1 (MQ=255)
                                                                                                                                               gaaa‑aaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGaa   <  4:58979/147‑1 (MQ=255)
                                                                                                                                               gaaa‑aaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGaa   >  3:268174/4‑150 (MQ=255)
                                                                                                                                                aaa‑aaaGATAACGACTCTTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAAAATTAATGATGAATTGGGTGAAGTGCTGATTGaaa  <  2:1387108/148‑1 (MQ=255)
                                                                                                                                                aaa‑aaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGaaa  <  2:1282733/148‑1 (MQ=255)
                                                                                                                                                |||                                                                                                                                                    
TGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑C‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAA  >  NC_000913_3_pae_tpiA/1543880‑1544170

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A