Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A1 F1 I1 R1 1357 179.3 9500450 96.1% 9129932 93.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,458,650 +G intergenic (‑161/+20) b2342 ← / ← b2343 putative acyltransferase/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,458,6461.G99.0% 308.9 / ‑3.6 97intergenic (‑157/+24)b2342/b2343putative acyltransferase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base G (49/47);  total (50/47)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

Only 100 of 107 total aligned reads displayed.

ACATTTAGCCAAGTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACA‑GGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCGATATCC  >  NC_000913/2458554‑2458733
                                                                                             |                                                                                       
aCATTTAGCCAAGTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACa                                                                                          >  1:3111282/1‑93 (MQ=255)
aCATTTAGCCAAGGGGAGAAAAGGGAAAGGGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACa                                                                                          <  1:1672548/93‑1 (MQ=255)
 cATTTAGCCAAGTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACA‑g                                                                                        >  2:2802591/1‑93 (MQ=255)
 cATTTAGCCAAGTGGAGAAAAGGGAAAGTGGAAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACA‑g                                                                                        <  2:4291839/93‑1 (MQ=255)
  aTTTAGCCAAGTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACA‑gg                                                                                       <  1:464940/93‑1 (MQ=255)
   tttAGCCAAGTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACA‑ggg                                                                                      <  1:3127469/93‑1 (MQ=255)
   ttgcgCCAGGTGGAAAAAGGGGAGCGGGGGAGCTAATACAGAGAGAGAAAAAAAGAAAAAAAGAGAACACGCCCCTGCCAGCAACTGACA‑ggg                                                                                      <  2:4173941/89‑1 (MQ=255)
      aGCCAAGTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACA‑gggggc                                                                                   >  2:4391179/1‑91 (MQ=255)
          aaGTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGcgtac                                                                                >  1:4364526/1‑93 (MQ=255)
          aaGTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGcgtac                                                                                >  1:620428/1‑93 (MQ=255)
          aaGTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGcgtac                                                                                >  2:194717/1‑93 (MQ=255)
          aaGTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGcgtac                                                                                >  2:1892193/1‑93 (MQ=255)
           aGTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGcgtacg                                                                               >  2:2446599/1‑93 (MQ=255)
            gTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGcgtacgt                                                                              <  1:181275/93‑1 (MQ=255)
            gTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGcgtacgt                                                                              >  1:2517806/1‑93 (MQ=255)
            gTGAAGAAAGGGAAAAGGGGGAGCTATAACAAAGAAAAAAAAAAAAAAAAAAAAAAAAAACGCCCCTGCCAGCAACTGACAGGGGGcgtacgt                                                                              <  1:863243/93‑1 (MQ=255)
                agaAAAGAGAAAGAGAGAGCTATGACACAGAGAGAAAAGAAGAAGAAAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTAccc                                                                          <  2:1958471/93‑1 (MQ=255)
                 gaAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCg                                                                         <  1:2096129/93‑1 (MQ=255)
                  aaaaGGGAAAGTGGGAGCTATGACAAAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCga                                                                        <  1:2778976/93‑1 (MQ=255)
                    aaGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCgaga                                                                      >  1:2521285/1‑93 (MQ=255)
                     aGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGagag                                                                     <  2:3245649/93‑1 (MQ=255)
                      gggAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAgg                                                                    <  1:1602748/93‑1 (MQ=255)
                       ggAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGa                                                                   <  1:1603031/93‑1 (MQ=255)
                        gAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAGCGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGaa                                                                  <  1:483373/93‑1 (MQ=255)
                         aaaGTGGGAGCTATGCCACGGAGAGAAAGGAAGCAGAGAAAGGAAAACGCCCCTGCCAGCGACTGACAGGGGGCGTACGTACCCGAGCGGact                                                                 <  1:4224990/93‑3 (MQ=255)
                         aaaGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAAt                                                                 <  2:3763175/93‑1 (MQ=255)
                         aaaGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAAt                                                                 >  1:98074/1‑93 (MQ=255)
                         aaaGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAAt                                                                 >  1:846947/1‑93 (MQ=255)
                         aaaGTGGGAGCTATGACACAGAGAAAAAAGAAGAAGAGAAAAGAAAACTCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAAt                                                                 <  1:4092439/93‑1 (MQ=255)
                           aGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTa                                                               >  1:4430078/1‑93 (MQ=255)
                             tGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAAc                                                             <  1:1143836/93‑1 (MQ=255)
                              gggAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACg                                                            >  1:1217339/1‑93 (MQ=255)
                              gggAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACg                                                            >  2:3905524/1‑93 (MQ=255)
                                gAGCTATGACACAGAGAGAAAAGAAAAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCa                                                          <  2:4332583/93‑1 (MQ=255)
                                  gCTATGACACAGAGAGAAATGAAGAAGAGAAAAGAATACGCCCGTGCCAGCAACTGACAGGGGGCGTCCGTCCCCGAGAGGAATTAACGCAGa                                                        <  2:3292338/93‑1 (MQ=255)
                                  gCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGa                                                        <  1:3158620/93‑1 (MQ=255)
                                     aTGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGAccc                                                     <  2:4112819/93‑1 (MQ=255)
                                       gACACAGAGAGAAAAGAAGAAAAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAg                                                   <  1:3576472/93‑1 (MQ=255)
                                         cacaGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTTCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCt                                                 >  1:463570/1‑93 (MQ=255)
                                          acaGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTTCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTg                                                >  2:4211523/1‑93 (MQ=255)
                                          acaGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTg                                                <  1:2953287/93‑1 (MQ=255)
                                             gagagaAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGaa                                             >  1:556054/1‑93 (MQ=255)
                                               gagaAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGaaaa                                           >  1:4246512/1‑93 (MQ=255)
                                                   aaaGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAg                                       >  2:3251357/1‑93 (MQ=255)
                                                    aagaagaagAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGc                                      >  2:1198224/1‑93 (MQ=255)
                                                     agaagaagaGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCa                                     >  2:4170519/1‑93 (MQ=255)
                                                     agaagaagaGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCa                                     >  2:1820666/1‑93 (MQ=255)
                                                      gaagaagaGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCAt                                    >  2:2034128/1‑93 (MQ=255)
                                                      gaagaagaGAAAAGAAAACGCCCCTGCCAGCAACTGACA‑GGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCAtt                                   >  1:2343491/1‑93 (MQ=255)
                                                      aaagaagaGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCAt                                    <  1:2045127/92‑1 (MQ=255)
                                                        agaagaGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCAttt                                  >  2:1355093/1‑93 (MQ=255)
                                                         gaagaGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTc                                 <  1:4697878/93‑1 (MQ=255)
                                                         gaagaGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTc                                 >  2:1879324/1‑93 (MQ=255)
                                                          aagaGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCa                                <  2:3164620/93‑1 (MQ=255)
                                                          aagaGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCa                                <  1:1931453/93‑1 (MQ=255)
                                                           agagAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAg                               >  1:1249386/1‑93 (MQ=255)
                                                            gagaAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGc                              >  2:1605891/1‑93 (MQ=255)
                                                            gagaAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGc                              <  1:3994913/93‑1 (MQ=255)
                                                             agaaaagaaaACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCt                             <  2:1195121/93‑1 (MQ=255)
                                                             agaaaagaaaACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCt                             >  2:303089/1‑93 (MQ=255)
                                                              gaaaagaaaaCGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCATCtt                            <  2:4646822/93‑1 (MQ=255)
                                                              aaaaagaaaaCGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCtt                            <  1:966759/92‑1 (MQ=255)
                                                                aaagaaaaCGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCg                          >  1:4151779/1‑93 (MQ=255)
                                                                aaagaaaaCGCCCCTGCCAGCAACTGACAGGGGGCGTACATACCCGAGAGGAATTAACGCAGACCCAGCTGGCAAATCAGCATTTCAGCTTCg                          >  1:4235074/1‑93 (MQ=255)
                                                                 aagaaaaCGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGc                         <  1:4544679/93‑1 (MQ=255)
                                                                  agaaaaCGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCa                        <  2:3111282/93‑1 (MQ=255)
                                                                   gaaaaCGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAg                       <  2:2465993/93‑1 (MQ=255)
                                                                    aaacCGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAgg                      <  1:2312266/93‑1 (MQ=255)
                                                                     aatcGCCCGTGCCAGCAGCTGGGAGGGGGTGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGc                     <  1:3727970/90‑1 (MQ=255)
                                                                     aaccGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGc                     <  1:3727969/90‑1 (MQ=255)
                                                                       aCGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCaa                   >  2:4501044/1‑93 (MQ=255)
                                                                        cGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAAATAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCaaa                  <  1:4235602/93‑1 (MQ=255)
                                                                        cGCCCCTGCCAGCAACTCACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCaaa                  >  2:4235887/1‑93 (MQ=255)
                                                                         gCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCaaaa                 >  1:441941/1‑93 (MQ=255)
                                                                         gCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCaaaa                 <  1:2179917/93‑1 (MQ=255)
                                                                           cccTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGt               <  1:4131202/93‑1 (MQ=255)
                                                                           cccTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGt               <  1:3565113/93‑1 (MQ=255)
                                                                           cccTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGt               >  2:1261333/1‑93 (MQ=255)
                                                                            ccTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGta              >  2:3650085/1‑92 (MQ=255)
                                                                            ccTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTg              >  2:2657578/1‑93 (MQ=255)
                                                                             cTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGa             <  1:2315181/93‑1 (MQ=255)
                                                                             cTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGa             >  2:4404689/1‑93 (MQ=255)
                                                                             cTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGa             <  1:3944364/93‑1 (MQ=255)
                                                                              tGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGaa            <  2:2259173/93‑1 (MQ=255)
                                                                              tGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGaa            >  1:408768/1‑93 (MQ=255)
                                                                               gCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGaaa           <  1:243335/93‑1 (MQ=255)
                                                                               gCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGaaa           <  2:1782544/93‑1 (MQ=255)
                                                                               gCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGaaa           <  1:618886/93‑1 (MQ=255)
                                                                                ccAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAAt          <  2:2864114/93‑1 (MQ=255)
                                                                                 cAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATc         >  2:1005001/1‑93 (MQ=255)
                                                                                   gCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATcta       >  1:3104972/1‑91 (MQ=255)
                                                                                   gCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCGa       >  2:3692629/1‑93 (MQ=255)
                                                                                    cAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCGat      <  2:4199211/93‑1 (MQ=255)
                                                                                    cAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCGat      <  1:830458/93‑1 (MQ=255)
                                                                                     aaCTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCGata     >  2:3883707/1‑93 (MQ=255)
                                                                                      aCTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCGatat    >  2:1586900/1‑93 (MQ=255)
                                                                                       cTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCGATATc   >  2:1851921/1‑93 (MQ=255)
                                                                                       cTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCGATATc   >  2:1851920/1‑93 (MQ=255)
                                                                                       cTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCGATATc   >  1:1461287/1‑93 (MQ=255)
                                                                                        tGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCGATATcc  <  1:3226690/93‑1 (MQ=255)
                                                                                             |                                                                                       
ACATTTAGCCAAGTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACA‑GGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCGATATCC  >  NC_000913/2458554‑2458733

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TTTAGCCAAGTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACA‑GGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCGATATCCAGGCGCA  >  NC_000913/2458557‑2458740
                                                                                              |                                                                                          
TTTAGCCAAGTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACA‑GGGG                                                                                            <  SRR4302544.3157190/94‑1 (MQ=60)
     CCAAGTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCCGCAACTGACAGGGGGCGTA                                                                                        >  SRR4302544.1755485/1‑94 (MQ=60)
      CAAGTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTAC                                                                                       >  SRR4302544.626514/1‑94 (MQ=60)
      CAAGTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTAC                                                                                       >  SRR4302544.4408802/1‑94 (MQ=60)
        AGTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGT                                                                                     >  SRR4302544.2541985/1‑94 (MQ=60)
         gtgaagaaagggaaaagggggagctataacaaagaaaaaaaaaaaaaaaaaaaaaaAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTA                                                                                    <  SRR4302544.871782/38‑1 (MQ=56)
         GTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTA                                                                                    <  SRR4302544.183067/94‑1 (MQ=60)
              GAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGA                                                                               <  SRR4302544.2116301/94‑1 (MQ=60)
               AAAAGGGAAAGTGGGAGCTATGACAAAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAG                                                                              <  SRR4302544.2805711/94‑1 (MQ=60)
                AAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGA                                                                             >  SRR4302544.2545503/1‑94 (MQ=60)
                   GGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGA                                                                          <  SRR4302544.1618551/94‑1 (MQ=60)
                    GGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAA                                                                         <  SRR4302544.1618835/94‑1 (MQ=60)
                     GAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAGCGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAAT                                                                        <  SRR4302544.488106/94‑1 (MQ=60)
                     GAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAAT                                                                        >  SRR4302544.855309/1‑94 (MQ=60)
                     GAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAAT                                                                        >  SRR4302544.98972/1‑94 (MQ=60)
                      AAAGTGGGAGCTATGACACAGAGAAAAAAGAAGAAGAGAAAAGAAAACTCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATT                                                                       <  SRR4302544.4133150/94‑1 (MQ=60)
                       AAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTA                                                                      >  SRR4302544.4474777/1‑94 (MQ=60)
                          TGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACG                                                                   >  SRR4302544.1229383/1‑94 (MQ=60)
                          TGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACG                                                                   <  SRR4302544.1155210/94‑1 (MQ=60)
                               GCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGAC                                                              <  SRR4302544.3188660/94‑1 (MQ=60)
                                 TATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCC                                                            >  SRR4302544.4599761/1‑94 (MQ=60)
                                    GACACAGAGAGAAAAGAAGAAAAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGC                                                         <  SRR4302544.3610777/94‑1 (MQ=60)
                                     ACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTTCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCT                                                        >  SRR4302544.468120/1‑94 (MQ=60)
                                       ACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGG                                                      <  SRR4302544.2981655/94‑1 (MQ=60)
                                         AGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAA                                                    >  SRR4302544.561494/1‑94 (MQ=60)
                                           AGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAA                                                  >  SRR4302544.4289804/1‑94 (MQ=60)
                                                  AGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACA‑GGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATT                                          >  SRR4302544.2365688/1‑94 (MQ=60)
                                                   AAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATT                                          <  SRR4302544.2064841/94‑1 (MQ=60)
                                                     AGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTC                                        <  SRR4302544.3782955/94‑1 (MQ=60)
                                                      GAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCA                                       <  SRR4302544.4744253/94‑1 (MQ=60)
                                                       AAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAG                                      >  SRR4302544.1261684/1‑94 (MQ=60)
                                                       AAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAG                                      <  SRR4302544.1950144/94‑1 (MQ=60)
                                                         GAGAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCT                                    <  SRR4302544.4034676/94‑1 (MQ=60)
                                                           AAAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTC                                  <  SRR4302544.976239/94‑1 (MQ=60)
                                                            AAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCG                                 >  SRR4302544.4192893/1‑94 (MQ=60)
                                                            AAAAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACATACCCGAGAGGAATTAACGCAGACCCAGCTGGCAAATCAGCATTTCAGCTTCG                                 >  SRR4302544.4278240/1‑94 (MQ=60)
                                                              AAGAAAACGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCA                               <  SRR4302544.4590081/94‑1 (MQ=60)
                                                                 AAACCGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGC                            <  SRR4302544.2334136/94‑1 (MQ=60)
                                                                  AACCGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCA                           <  SRR4302544.3765037/94‑1 (MQ=60)
                                                                     CGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAA                        >  SRR4302544.446368/1‑94 (MQ=60)
                                                                     CGCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAAATAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAA                        <  SRR4302544.4278771/94‑1 (MQ=60)
                                                                      GCCCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAG                       <  SRR4302544.2200558/94‑1 (MQ=60)
                                                                        CCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTG                     <  SRR4302544.4172153/94‑1 (MQ=60)
                                                                        CCCTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTG                     <  SRR4302544.3599294/94‑1 (MQ=60)
                                                                          CTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAA                   >  SRR4302544.412929/1‑94 (MQ=60)
                                                                          CTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAA                   <  SRR4302544.2337094/94‑1 (MQ=60)
                                                                          CTGCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAA                   <  SRR4302544.3983551/94‑1 (MQ=60)
                                                                            GCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAAT                 <  SRR4302544.245866/94‑1 (MQ=60)
                                                                            GCCAGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAAT                 <  SRR4302544.624961/94‑1 (MQ=60)
                                                                               AGCAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCTA              >  SRR4302544.3134521/1‑94 (MQ=60)
                                                                                 CAACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCGATA            <  SRR4302544.838622/94‑1 (MQ=60)
                                                                                  AACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCGATAT           >  SRR4302544.2374534/1‑94 (MQ=60)
                                                                                   ACTGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCGATATC          >  SRR4302544.1475784/1‑94 (MQ=60)
                                                                                     TGACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCGATATCCA        <  SRR4302544.3257543/94‑1 (MQ=60)
                                                                                      GACAGGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCGATATCCAG       <  SRR4302544.4106796/94‑1 (MQ=60)
                                                                                         agGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCACAAGTGAAATCGATATCCAGGCG    >  SRR4302544.230421/3‑94 (MQ=60)
                                                                                         agGGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCGATATCCAGGCG    >  SRR4302544.230422/3‑94 (MQ=60)
                                                                                           GGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCGATATCCAGGCGCA  <  SRR4302544.1479103/94‑1 (MQ=60)
                                                                                              |                                                                                          
TTTAGCCAAGTGGAGAAAAGGGAAAGTGGGAGCTATGACACAGAGAGAAAAGAAGAAGAGAAAAGAAAACGCCCCTGCCAGCAACTGACA‑GGGGCGTACGTACCCGAGAGGAATTAACGCAGACCCAGCTGGAAAATCAGCATTTCAGCTTCGCAGGCAAAAGTGAAATCGATATCCAGGCGCA  >  NC_000913/2458557‑2458740

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 2 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑