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
A11 F256 I0 R1 328 102.7 5123138 93.4% 4785010 99.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 4,017,924 G→A 100% D198N (GAC→AAC)  rmuC → DNA recombination protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,017,9240GA96.8% 287.0 / ‑0.1 92D198N (GAC→AAC) rmuCDNA recombination protein
Reads supporting (aligned to +/- strand):  ref base G (2/1);  new base A (42/47);  total (44/48)
Fisher's exact test for biased strand distribution p-value = 6.05e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.09e-01

AGAACGCCATACCCTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCGACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGTATGAATATGAAACCCAGGTCAG  >  NC_000913/4017827‑4018021
                                                                                                 |                                                                                                 
aGAACGCCATACCCTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAAc                                                                                                 <  1:1733156/100‑1 (MQ=255)
aGAACGCCATACCCTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAAc                                                                                                 <  2:268487/100‑1 (MQ=255)
aGAACGCCATACCCTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAAc                                                                                                 <  2:1762059/100‑1 (MQ=255)
 gAACACCATACCCTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACa                                                                                                >  1:839615/1‑100 (MQ=255)
  aaCGCCATACCCTGACCCACGAAATTCGCAAGCTCCAGCAACTCAACGCGCAAAGGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGcaacaa                                                                                               <  2:1818485/100‑1 (MQ=255)
   aCGCCATACCCTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAAt                                                                                              <  1:2495307/100‑1 (MQ=255)
    cGCCATACCCTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAAt                                                                                              <  1:1301755/99‑1 (MQ=255)
     gCCATACCCTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATaa                                                                                            <  1:696106/100‑1 (MQ=255)
        aTACCCTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAAc                                                                                         <  2:1717702/100‑1 (MQ=255)
        aTACCCTGACCCACGAAAGTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAAc                                                                                         <  2:957764/100‑1 (MQ=255)
           cccTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCa                                                                                      >  1:2389591/1‑100 (MQ=255)
            ccTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAACTGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCa                                                                                      >  1:686573/1‑99 (MQ=255)
                aCCCACGGAATCCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCa                                                                                 >  2:1341832/1‑100 (MQ=255)
                  ccACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAAc                                                                               >  1:2232953/1‑100 (MQ=255)
                   cACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACt                                                                              >  2:234196/1‑100 (MQ=255)
                   cACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACt                                                                              >  2:1437737/1‑100 (MQ=255)
                    aCGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTg                                                                             >  2:1185779/1‑100 (MQ=255)
                        aaTTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGc                                                                         <  1:1329270/100‑1 (MQ=255)
                           tCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAg                                                                      <  1:2035937/100‑1 (MQ=255)
                            cGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAgg                                                                     >  2:2498149/1‑100 (MQ=255)
                             gCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGgt                                                                    <  2:1985455/100‑1 (MQ=255)
                             gCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGgt                                                                    >  1:2386579/1‑100 (MQ=255)
                             gCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGgt                                                                    >  1:296225/1‑100 (MQ=255)
                                 tctcCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGgtagta                                                                <  2:296221/100‑1 (MQ=255)
                                  ctcCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGCCAAATGGGGCGAGGTAGTAt                                                               <  2:622836/100‑1 (MQ=255)
                                   tcCAGCAACTCAACGCGCAAATGGCCCAGGGAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTAtt                                                              >  1:1309530/1‑100 (MQ=255)
                                   tcCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTAtt                                                              >  1:2306602/1‑100 (MQ=255)
                                   tcCAGCAACTCAACGCGCAAAGGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTAtt                                                              <  2:941089/100‑1 (MQ=255)
                                    ccAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTAtt                                                              <  1:1051774/99‑1 (MQ=255)
                                    ccAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTg                                                             >  1:1456372/1‑100 (MQ=255)
                                       gCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGAcg                                                          >  1:248964/1‑100 (MQ=255)
                                       gCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGAcg                                                          >  1:1078292/1‑100 (MQ=255)
                                        cAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGAcgc                                                         >  1:213373/1‑100 (MQ=255)
                                         aaCTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGAcgcg                                                        <  1:1198748/100‑1 (MQ=255)
                                         aaCTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGAcgcg                                                        >  1:1870446/1‑100 (MQ=255)
                                          aCTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGACAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCgg                                                       >  2:2417731/1‑100 (MQ=255)
                                          aCTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCgg                                                       <  2:207068/100‑1 (MQ=255)
                                          aCTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCgg                                                       <  2:150974/100‑1 (MQ=255)
                                           cTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGACAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCggg                                                      >  2:2182568/1‑100 (MQ=255)
                                              aaCGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGc                                                   <  2:426416/100‑1 (MQ=255)
                                               aCGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCt                                                  >  2:1893919/1‑100 (MQ=255)
                                                cgcgCAAATGGCCCAGGAAGCGTTCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTg                                                 >  2:1483946/1‑100 (MQ=255)
                                                  cgcAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGa                                               >  1:1054397/1‑100 (MQ=255)
                                                  cgcAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGa                                               >  1:2441450/1‑100 (MQ=255)
                                                    cAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAgg                                             >  1:1038100/1‑100 (MQ=255)
                                                    cAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAgg                                             >  1:2173507/1‑100 (MQ=255)
                                                     aaaTGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGc                                            <  2:1180751/100‑1 (MQ=255)
                                                      aaTGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCt                                           <  1:1213273/100‑1 (MQ=255)
                                                         ggCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTcc                                        <  1:1272211/100‑1 (MQ=255)
                                                         ggCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTcc                                        <  1:1858426/100‑1 (MQ=255)
                                                         ggCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTcc                                        <  1:1782561/100‑1 (MQ=255)
                                                          gCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCg                                       >  2:1750372/1‑100 (MQ=255)
                                                           cccAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCgg                                      <  2:1328652/100‑1 (MQ=255)
                                                           cccAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCgg                                      <  1:606994/100‑1 (MQ=255)
                                                           cccAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCgg                                      <  1:1946434/100‑1 (MQ=255)
                                                            ccAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGt                                     >  1:2131227/1‑100 (MQ=255)
                                                             cAGGAAGCGATCAACCTGACTCTCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTAAAGACGCGGGGGCAGGAGGCTTCCgg                                      >  2:935707/1‑98 (MQ=255)
                                                             cAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTc                                    <  1:218906/100‑1 (MQ=255)
                                                             cAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTc                                    <  1:900477/100‑1 (MQ=255)
                                                             cAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTAATGACGCGGGTGCCGGAGGCTTCCGGTc                                    >  2:1113314/1‑100 (MQ=255)
                                                              aGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCt                                   <  1:815948/100‑1 (MQ=255)
                                                               ggAAGCGATGAAGCGGACCTGCGCGCTGAAAGGCAACAATAAGACCCAGGGCATCGGGGGCGAGGTAGTATTGACGCGGGGGCTGGAGGCTTCCGGTCTg                                  <  2:2399704/100‑1 (MQ=255)
                                                               ggAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTg                                  <  1:2102747/100‑1 (MQ=255)
                                                                 aaGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCg                                >  2:1381685/1‑100 (MQ=255)
                                                                  aGCGATCACCCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCg                                <  2:699541/99‑1 (MQ=255)
                                                                    cGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGa                             >  2:949999/1‑100 (MQ=255)
                                                                       tCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTTGAGGCTTCCGGTCTGCGTGAAgg                          <  1:897769/100‑1 (MQ=255)
                                                                       tCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAgg                          <  1:143908/100‑1 (MQ=255)
                                                                        cAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAggg                         <  1:358874/100‑1 (MQ=255)
                                                                        cAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAggg                         <  1:1381694/100‑1 (MQ=255)
                                                                         aaCCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGt                        >  2:2366165/1‑100 (MQ=255)
                                                                          aCCTGCCGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCCACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCAGTCTGTGTGAAGGGta                       >  2:18266/1‑100 (MQ=255)
                                                                          aCCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGTTTCCGGTCTGCGTGAAGGGta                       >  1:970957/1‑100 (MQ=255)
                                                                          aCCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGta                       >  1:469521/1‑100 (MQ=255)
                                                                          aCCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGta                       >  2:2372401/1‑100 (MQ=255)
                                                                           ccTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGtat                      <  1:306014/100‑1 (MQ=255)
                                                                            cTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGtatg                     <  1:732472/100‑1 (MQ=255)
                                                                              gccgcgcgcgCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGtatgn                    <  2:755969/97‑2 (MQ=255)
                                                                              gACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGtatgaa                   >  2:1643824/1‑100 (MQ=255)
                                                                                  cgcgcgcTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGtatgaatatg               <  1:1320282/100‑1 (MQ=255)
                                                                                  cgcgcgcTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGtatgaatatg               <  1:567051/100‑1 (MQ=255)
                                                                                  cgcgcgcTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGtatgaatatg               <  1:1089787/100‑1 (MQ=255)
                                                                                    cgcgcTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGtatgaatatgaa             <  1:1896201/100‑1 (MQ=255)
                                                                                     gcgcTGAAAGGCGACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGTATGAATATGaaa            >  2:558907/1‑100 (MQ=255)
                                                                                        cttaaaGACAACAATAAAACCCAGGGTAACTGCCGCGAGGTAGTATTTACGCCGGTGCTGGAGACTTCCGGTCTGCATGAAGGGtatgaatatga              >  2:540197/4‑95 (MQ=255)
                                                                                        cTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGTATGAATATGAAAccc         <  2:1476533/100‑1 (MQ=255)
                                                                                         tGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGTATGAATATGAAACCCa        >  2:1272327/1‑100 (MQ=255)
                                                                                           aaaGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGTATGAATATGAAACCCAgg      <  1:445075/100‑1 (MQ=255)
                                                                                            aaGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGTATGAATATGAAACCCAgg      <  2:1731690/99‑1 (MQ=255)
                                                                                            aaGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGTATGAATATGAAACCCAGGt     >  1:813393/1‑100 (MQ=255)
                                                                                             aGGCGACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGTATGAATATGAAACCCAGGTc    <  1:558914/100‑1 (MQ=255)
                                                                                              ggCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGTATGAATATGAAACCCAGGTCa   >  2:2554915/1‑100 (MQ=255)
                                                                                               gCGACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGGATGAATATGAAACCCAGGTCAg  >  2:2550046/1‑100 (MQ=255)
                                                                                                 |                                                                                                 
AGAACGCCATACCCTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCGACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGTATGAATATGAAACCCAGGTCAG  >  NC_000913/4017827‑4018021

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